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Journal Articles

Abstract 1459: Identification of transcription factor enrichments in HPV+ head and neck cancer using ChIP-seq and cistrome analysis

Fernando Zamuner, Spencer S. Chan, Michael Kessler, Ilya Vorontsov, Ludmila Danilova, Rossin Erbe, Dylan Kelley, Theresa Guo, Eddie Imada, Elana J. Fertig, Ivan Kulakovskiy, Alexander Favorov, Daria A. Gaykalova

Cancer Res (2022) 82 (12_Supplement): 1459.

DOI: https://doi.org/10.1158/1538-7445.AM2022-1459

Published: 15 June 2022

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Journal Articles

Abstract 3024: Transcriptional and epigenetic regulation of resistance markers in cetuximab sensitive HNSCC cells

Luciane T. Kagohara, Fernando Zamuner, Michael Considine, Genevieve Stein-O'Brien, Thomas Sherman, Daria A. Gaykalova, Elana J. Fertig

Cancer Res (2019) 79 (13_Supplement): 3024.

DOI: https://doi.org/10.1158/1538-7445.AM2019-3024

Published: 01 July 2019

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Journal Articles

Abstract 3399: Uncovering hidden sources of transcriptional dysregulation arising from inter- and intra-tumor heterogeneity

Bahman Afsari, Leslie Cope, Daria A. Gaykalova, Donald Geman, Sidharth Puram, Loyal A. Goff, Alexander Favorov, Elana Judith Fertig

Cancer Res (2019) 79 (13_Supplement): 3399.

DOI: https://doi.org/10.1158/1538-7445.AM2019-3399

Published: 01 July 2019

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Journal Articles

Abstract 5206: Role of super-enhancers in HPV+ head and neck squamous cell carcinoma

Fernando T. Zamuner, Ilya Vorontsov, Emily Flam, Vera Mukhina, Ludmila Danilova, Tingting Ou, Elena Stavrovskaya, Theresa Guo, Eric Windsor, Dylan Z. Kelley, Michael Parfenov, Michael Considine, Elana J. Fertig, Alexander Favorov, Daria A. Gaykalova

Cancer Res (2019) 79 (13_Supplement): 5206.

DOI: https://doi.org/10.1158/1538-7445.AM2019-5206

Published: 01 July 2019

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Journal Articles

Abstract 3320: Discovery and development of DNA methylation biomarkers in human papillomavirus related oropharyngeal squamous cell carcinoma

Shuling Ren, Daria A. Gaykalova, Theresa W. Guo, Alexander V. Favorov, Elana J. Fertig, Zubair Khan, Peter M. DeJong, Mizuo Ando, Chao Liu, Akihiro Sakai, Takahito Fukusumi, Sunny Haft, Sayed Sadat, J Silvio Gutkind, Wayne M. Koch, Joseph A. Califano

Cancer Res (2018) 78 (13_Supplement): 3320.

DOI: https://doi.org/10.1158/1538-7445.AM2018-3320

Published: 01 July 2018

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Journal Articles

Abstract 364: Differentially methylated super-enhancers regulate gene expression in human papillomavirus-related head and neck squamous cell carcinoma

Emily L. Flam, Dylan Z. Kelley, Elena Stavrovskaya, Ludmila Danilova, Theresa Guo, Michael Considine, Jiang Qian, Joseph A. Califano, Alexander V. Favorov, Elana J. Fertig, Daria A. Gaykalova

Cancer Res (2018) 78 (13_Supplement): 364.

DOI: https://doi.org/10.1158/1538-7445.AM2018-364

Published: 01 July 2018

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Journal Articles

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

Cancer Res (2017) 77 (23): 6538–6550.

DOI: https://doi.org/10.1158/0008-5472.CAN-17-0833

Published: 30 November 2017

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Includes: Supplementary data

Journal Articles

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers

Theresa Guo, Akihiro Sakai, Bahman Afsari, Michael Considine, Ludmila Danilova, Alexander V. Favorov, Srinivasan Yegnasubramanian, Dylan Z. Kelley, Emily Flam, Patrick K. Ha, Zubair Khan, Sarah J. Wheelan, J. Silvio Gutkind, Elana J. Fertig, Daria A. Gaykalova, Joseph Califano

Cancer Res (2017) 77 (19): 5248–5258.

DOI: https://doi.org/10.1158/0008-5472.CAN-16-3106

Published: 01 October 2017

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Includes: Supplementary data

Journal Articles

Abstract 4474: Functional characterization of alternatively spliced GSN in head and neck cancer

Dylan Z. Kelley, Emily L. Flam, Theresa Guo, Craig Bohrson, Michael Considine, Ludmila V. Danilova, Justin A. Bishop, Chi Zhang, Wayne M. Koch, David Sidransky, William Westra, Sarah Wheelan, Liliana Florea, Elana J. Fertig, Joseph A. Califano, Daria A. Gaykalova

Cancer Res (2017) 77 (13_Supplement): 4474.

DOI: https://doi.org/10.1158/1538-7445.AM2017-4474

Published: 01 July 2017

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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

Cancer Res (2017) 77 (13_Supplement): 3577.

DOI: https://doi.org/10.1158/1538-7445.AM2017-3577

Published: 01 July 2017

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Journal Articles

Abstract 3353: An epigenetic biomarker panel in HPV related oropharyngeal squamous cell carcinoma

Shuling Ren, Daria A. Gaykalova, Theresa Guo, Zubair Khan, Mizuo Ando, Sunny Haft, Joseph A. Califano

Cancer Res (2017) 77 (13_Supplement): 3353.

DOI: https://doi.org/10.1158/1538-7445.AM2017-3353

Published: 01 July 2017

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Journal Articles

Abstract 2424: The in-parallel whole-genome ChIP-Seq analysis of primary tissues, patient derived xenografts, and cancer cell lines from HPV-relative HNSCC samples

Dylan Z. Kelley, Emily L. Flam, Hildegard A. Wulf, Theresa Guo, Evgeny Izumchenko, Dzov A. Singman, Ludmila V. Danilova, Elena D. Stavrovskaya, Michael Considine, Justin A. Bishop, William H. Westra, Zubair Khan, Wayne M. Koch, David Sidransky, Sarah Wheelan, Joseph A. Califano, Alexander V. Favorov, Elana J. Fertig, Daria A. Gaykalova

Cancer Res (2017) 77 (13_Supplement): 2424.

DOI: https://doi.org/10.1158/1538-7445.AM2017-2424

Published: 01 July 2017

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Journal Articles

Abstract 2880: The discovery of novel GSN alternative splicing in head and neck squamous cell carcinoma

Cancer Res (2016) 76 (14_Supplement): 2880.

DOI: https://doi.org/10.1158/1538-7445.AM2016-2880

Published: 15 July 2016

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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

Cancer Res (2016) 76 (14_Supplement): 777.

DOI: https://doi.org/10.1158/1538-7445.AM2016-777

Published: 15 July 2016

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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

Cancer Res (2015) 75 (15_Supplement): 815.

DOI: https://doi.org/10.1158/1538-7445.AM2015-815

Published: 01 August 2015

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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

Cancer Res (2014) 74 (19_Supplement): 3409.

DOI: https://doi.org/10.1158/1538-7445.AM2014-3409

Published: 01 October 2014

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Journal Articles

Activation of the NOTCH Pathway in Head and Neck Cancer

Cancer Res (2014) 74 (4): 1091–1104.

DOI: https://doi.org/10.1158/0008-5472.CAN-13-1259

Published: 16 February 2014

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Includes: Supplementary data

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

Cancer Res (2013) 73 (8_Supplement): 3554.

DOI: https://doi.org/10.1158/1538-7445.AM2013-3554

Published: 15 April 2013

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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

Cancer Res (2013) 73 (8_Supplement): 2901.

DOI: https://doi.org/10.1158/1538-7445.AM2013-2901

Published: 15 April 2013

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Journal Articles

Abstract 4097: Integrative analysis of epigenetic and transcriptional alterations in head and neck squamous cell carcinomas

Daria A. Gaykalova, Rajita Vatapalli, Yingying Wei, Patrick Hennessey, Zubair Khan, William Westra, Tanbir Khan, David Zaboli, David Sidransky, Michael Ochs, Joseph A. Califano

Cancer Res (2012) 72 (8_Supplement): 4097.

DOI: https://doi.org/10.1158/1538-7445.AM2012-4097

Published: 15 April 2012

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NARROW

Abstract 1459: Identification of transcription factor enrichments in HPV+ head and neck cancer using ChIP-seq and cistrome analysis

Abstract 3024: Transcriptional and epigenetic regulation of resistance markers in cetuximab sensitive HNSCC cells

Abstract 3399: Uncovering hidden sources of transcriptional dysregulation arising from inter- and intra-tumor heterogeneity

Abstract 5206: Role of super-enhancers in HPV+ head and neck squamous cell carcinoma

Abstract 3320: Discovery and development of DNA methylation biomarkers in human papillomavirus related oropharyngeal squamous cell carcinoma

Abstract 364: Differentially methylated super-enhancers regulate gene expression in human papillomavirus-related head and neck squamous cell carcinoma

Integrated Analysis of Whole-Genome ChIP-Seq and RNA-Seq Data of Primary Head and Neck Tumor Samples Associates HPV Integration Sites with Open Chromatin Marks

A Novel Functional Splice Variant of AKT3 Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers

Abstract 4474: Functional characterization of alternatively spliced GSN in head and neck cancer

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

Abstract 3353: An epigenetic biomarker panel in HPV related oropharyngeal squamous cell carcinoma

Abstract 2424: The in-parallel whole-genome ChIP-Seq analysis of primary tissues, patient derived xenografts, and cancer cell lines from HPV-relative HNSCC samples

Abstract 2880: The discovery of novel GSN alternative splicing in head and neck squamous cell carcinoma

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

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

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

Activation of the NOTCH Pathway in Head and Neck Cancer

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

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.

Abstract 4097: Integrative analysis of epigenetic and transcriptional alterations in head and neck squamous cell carcinomas

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