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Journal Articles

Abstract 5698: Opposing roles of HOXC6 isoforms in promoting head and neck squamous cell carcinoma

Ishita Gupta, Subhendu Roy Choudhury, Anirudh Saxena, Madeleine Ndahayo, Vera Mukhina, Andrey Loginov, Nadya Vorobyeva, Daria A. Gaykalova

Cancer Res (2025) 85 (8_Supplement_1): 5698.

https://doi.org/10.1158/1538-7445.AM2025-5698

Published: 21 April 2025

View articletitled, Abstract 5698: Opposing roles of HOXC6 isoforms in promoting head and neck squamous cell carcinoma

Journal Articles

Abstract CT016: Immunomodulation of the tumor microenvironment of pancreatic ductal adenocarcinoma with histone deacetylase inhibition: Results of a phase 2 clinical trial of entinostat in combination with nivolumab

Cancer Res (2024) 84 (7_Supplement): CT016.

https://doi.org/10.1158/1538-7445.AM2024-CT016

Published: 05 April 2024

View articletitled, Abstract CT016: Immunomodulation of the tumor microenvironment of pancreatic ductal adenocarcinoma with histone deacetylase inhibition: Results of a phase 2 clinical trial of entinostat in combination with nivolumab

Journal Articles

Abstract 4352: A high rate of episomal HPV16 is present in head and neck squamous cell carcinoma tumors by long-read whole genome sequencing

Sonam Tulsyan, Vera Mukhina, Isabel Rodriguez, Subhendu R. Choudhury, Erin Allor, Kyle Hatte, Michael Dean, Daria A. Gaykalova

Cancer Res (2024) 84 (6_Supplement): 4352.

https://doi.org/10.1158/1538-7445.AM2024-4352

Published: 22 March 2024

View articletitled, Abstract 4352: A high rate of episomal HPV16 is present in head and neck squamous cell carcinoma tumors by long-read whole genome sequencing

Journal Articles

Abstract 7340: Investigating the function and impact of UBASH3B in head and neck squamous cell carcinoma and its implications for racial health disparities

Madeleine Ndahayo, Vera Mukhina, Ishita Gupta, Daria A. Gaykalova

Cancer Res (2024) 84 (6_Supplement): 7340.

https://doi.org/10.1158/1538-7445.AM2024-7340

Published: 22 March 2024

View articletitled, Abstract 7340: Investigating the function and impact of UBASH3B in head and neck squamous cell carcinoma and its implications for racial health disparities

Journal Articles

Abstract 315: HPV-related genome rearrangements in head and neck cancer cell lines

Vera Mukhina, Alexa Anderson, Daria A. Gaykalova

Cancer Res (2023) 83 (7_Supplement): 315.

https://doi.org/10.1158/1538-7445.AM2023-315

Published: 04 April 2023

View articletitled, Abstract 315: HPV-related genome rearrangements in head and neck cancer cell lines

Journal Articles

Abstract 1499: HOXC6 gene functions as an oncogenic driver in HPV+ head and neck squamous cell carcinoma (HNSCC)

Subhendu Roy Choudhury, Vera Mukhina, Iuliia Vyshkvorkina, Jessica Gore, Alexa Anderson, Daria A. Gaykalova

Cancer Res (2023) 83 (7_Supplement): 1499.

https://doi.org/10.1158/1538-7445.AM2023-1499

Published: 04 April 2023

View articletitled, Abstract 1499: HOXC6 gene functions as an oncogenic driver in HPV+ head and neck squamous cell carcinoma (HNSCC)

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.

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

Published: 15 June 2022

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

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.

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

Published: 01 July 2019

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

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.

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

Published: 01 July 2019

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

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.

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

Published: 01 July 2019

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

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.

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

Published: 01 July 2018

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

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.

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

Published: 01 July 2018

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

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.

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

Published: 30 November 2017

View articletitled, 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

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.

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

Published: 01 October 2017

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

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.

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

Published: 01 July 2017

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

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.

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 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.

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

Published: 01 July 2017

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

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.

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

Published: 01 July 2017

View articletitled, 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

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.

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

Published: 15 July 2016

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

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.

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

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Abstract 5698: Opposing roles of HOXC6 isoforms in promoting head and neck squamous cell carcinoma

Abstract CT016: Immunomodulation of the tumor microenvironment of pancreatic ductal adenocarcinoma with histone deacetylase inhibition: Results of a phase 2 clinical trial of entinostat in combination with nivolumab

Abstract 4352: A high rate of episomal HPV16 is present in head and neck squamous cell carcinoma tumors by long-read whole genome sequencing

Abstract 7340: Investigating the function and impact of UBASH3B in head and neck squamous cell carcinoma and its implications for racial health disparities

Abstract 315: HPV-related genome rearrangements in head and neck cancer cell lines

Abstract 1499: HOXC6 gene functions as an oncogenic driver in HPV+ head and neck squamous cell carcinoma (HNSCC)

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

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

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