Novel insight into mutational landscape of head and neck squamous cell carcinoma
Gaykalova, Daria A, Mambo, Elizabeth, Choudhary, Ashish, Houghton, Jeffery, Buddavarapu, Kalyan, Sanford, Tiffany, Darden, Will, Adai, Alex, Hadd, Andrew, Latham, Gary, Danilova, Ludmila V, Bishop, Justin, Li, Ryan J, Westra, William H, Hennessey, Patrick, Koch, Wayne M, Ochs, Michael F, Califano, Joseph A, Sun, Wenyue
Published in PloS one (25.03.2014)
Published in PloS one (25.03.2014)
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DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma
Finegersh, Andrey, Kulich, Scott, Guo, Theresa, Favorov, Alexander V, Fertig, Elana J, Danilova, Ludmila V, Gaykalova, Daria A, Califano, Joseph A, Duvvuri, Umamaheswar
Published in Scientific reports (09.11.2017)
Published in Scientific reports (09.11.2017)
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Journal Article
Correction: Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma
Gaykalova, Daria A, Mambo, Elizabeth, Choudhary, Ashish, Houghton, Jeffery, Buddavarapu, Kalyan, Sanford, Tiffany, Darden, Will, Adai, Alex, Hadd, Andrew, Latham, Gary, Danilova, Ludmila V, Bishop, Justin, Li, Ryan J, Westra, William H, Hennessey, Patrick, Koch, Wayne M, Ochs, Michael F, Califano, Joseph A, Sun, Wenyue
Published in PloS one (13.05.2020)
Published in PloS one (13.05.2020)
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Journal Article
Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis
Fertig, Elana J, Markovic, Ana, Danilova, Ludmila V, Gaykalova, Daria A, Cope, Leslie, Chung, Christine H, Ochs, Michael F, Califano, Joseph A
Published in PloS one (04.11.2013)
Published in PloS one (04.11.2013)
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Journal Article
Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance
Stein-O'Brien, Genevieve, Kagohara, Luciane T, Li, Sijia, Thakar, Manjusha, Ranaweera, Ruchira, Ozawa, Hiroyuki, Cheng, Haixia, Considine, Michael, Schmitz, Sandra, Favorov, Alexander V, Danilova, Ludmila V, Califano, Joseph A, Izumchenko, Evgeny, Gaykalova, Daria A, Chung, Christine H, Fertig, Elana J
Published in Genome medicine (23.05.2018)
Published in Genome medicine (23.05.2018)
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Multi-omic analyses of changes in the tumor microenvironment of pancreatic adenocarcinoma following neoadjuvant treatment with anti-PD-1 therapy
Li, Keyu, Tandurella, Joseph A., Gai, Jessica, Zhu, Qingfeng, Lim, Su Jin, Thomas, Dwayne L., Xia, Tao, Mo, Guanglan, Mitchell, Jacob T., Montagne, Janelle, Lyman, Melissa, Danilova, Ludmila V., Zimmerman, Jacquelyn W., Kinny-Köster, Benedict, Zhang, Tengyi, Chen, Linda, Blair, Alex B., Heumann, Thatcher, Parkinson, Rose, Durham, Jennifer N., Narang, Amol K., Anders, Robert A., Wolfgang, Christopher L., Laheru, Daniel A., He, Jin, Osipov, Arsen, Thompson, Elizabeth D., Wang, Hao, Fertig, Elana J., Jaffee, Elizabeth M., Zheng, Lei
Published in Cancer cell (14.11.2022)
Published in Cancer cell (14.11.2022)
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Epigenetic regulation of gene expression in cancer: techniques, resources and analysis
Kagohara, Luciane T, Stein-O’Brien, Genevieve L, Kelley, Dylan, Flam, Emily, Wick, Heather C, Danilova, Ludmila V, Easwaran, Hariharan, Favorov, Alexander V, Qian, Jiang, Gaykalova, Daria A, Fertig, Elana J
Published in Briefings in functional genomics (01.01.2018)
Published in Briefings in functional genomics (01.01.2018)
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Cytokines secreted by stromal cells in TNBC microenvironment as potential targets for cancer therapy
Malone, Marie K., Smrekar, Karly, Park, Sunju, Blakely, Brianna, Walter, Alec, Nasta, Nicholas, Park, Jay, Considine, Michael, Danilova, Ludmila V., Pandey, Niranjan B., Fertig, Elana J., Popel, Aleksander S., Jin, Kideok
Published in Cancer biology & therapy (02.06.2020)
Published in Cancer biology & therapy (02.06.2020)
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Journal Article
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
Kelley, Dylan Z, Flam, Emily L, Izumchenko, Evgeny, Danilova, Ludmila V, Wulf, Hildegard A, Guo, Theresa, Singman, Dzov A, Afsari, Bahman, Skaist, Alyza M, Considine, Michael, Welch, Jane A, Stavrovskaya, Elena, Bishop, Justin A, Westra, William H, Khan, Zubair, Koch, Wayne M, Sidransky, David, Wheelan, Sarah J, Califano, Joseph A, Favorov, Alexander V, Fertig, Elana J, Gaykalova, Daria A
Published in Cancer research (Chicago, Ill.) (01.12.2017)
Published in Cancer research (Chicago, Ill.) (01.12.2017)
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Journal Article
Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma
Kelley, Dylan Z, Flam, Emily L, Guo, Theresa, Danilova, Ludmila V, Zamuner, Fernando T, Bohrson, Craig, Considine, Michael, Windsor, Eric J, Bishop, Justin A, Zhang, Chi, Koch, Wayne M, Sidransky, David, Westra, William H, Chung, Christine H, Califano, Joseph A, Wheelan, Sarah, Favorov, Alexander V, Florea, Liliana, Fertig, Elana J, Gaykalova, Daria A
Published in Translational research : the journal of laboratory and clinical medicine (01.12.2018)
Published in Translational research : the journal of laboratory and clinical medicine (01.12.2018)
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Journal Article
Abstract A25: Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma
Guo, Theresa, Zambo, Kristina D. A., Zamuner, Fernando T., Ou, Tingting, Hopkins, Christopher, Kelley, Dylan Z., Wulf, Hildegard A., Danilova, Ludmila V., Considine, Michael, Sidransky, David, Favorov, Alexander V., Florea, Liliana, Fertig, Elana J., Gaykalova, Daria A.
Published in Clinical cancer research (15.06.2020)
Published in Clinical cancer research (15.06.2020)
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Abstract 05: Untangling the gene-epigenome networks: Timing of epigenetic regulation of gene expression in acquired cetuximab resistance gene programs
Stein-O'Brien, Genevieve, Kagohara, Luciane T., Li, Sijia, Thakar, Manjusha, Ranaweera, Ruchira, Considine, Michael, Danilova, Ludmila V., Ozawa, Hiroyuki, Califano, Joseph A., Gaykalova, Daria A., Ochs, Michael F., Chung, Christine H., Fertig, Elana J.
Published in Clinical cancer research (01.12.2017)
Published in Clinical cancer research (01.12.2017)
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Abstract 4474: Functional characterization of alternatively spliced GSN in head and neck cancer
Kelley, Dylan Z., Flam, Emily L., Guo, Theresa, Bohrson, Craig, Considine, Michael, Danilova, Ludmila V., Bishop, Justin A., Zhang, Chi, Koch, Wayne M., Sidransky, David, Westra, William, Wheelan, Sarah, Florea, Liliana, Fertig, Elana J., Califano, Joseph A., Gaykalova, Daria A.
Published in Cancer research (Chicago, Ill.) (01.07.2017)
Published in Cancer research (Chicago, Ill.) (01.07.2017)
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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
Kelley, Dylan Z., Flam, Emily L., Wulf, Hildegard A., Guo, Theresa, Izumchenko, Evgeny, Singman, Dzov A., Danilova, Ludmila V., Stavrovskaya, Elena D., Considine, Michael, Bishop, Justin A., Westra, William H., Khan, Zubair, Koch, Wayne M., Sidransky, David, Wheelan, Sarah, Califano, Joseph A., Favorov, Alexander V., Fertig, Elana J., Gaykalova, Daria A.
Published in Cancer research (Chicago, Ill.) (01.07.2017)
Published in Cancer research (Chicago, Ill.) (01.07.2017)
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Journal Article
Abstract 815: DTX1 is an epigenetically regulated tumor suppressor gene discovered by integrative analysis of epigenetic and transcriptional alterations in HNSCC
Gaykalova, Daria A., Zizkova, Veronika, Tiscareno, Ilse, Wei, Yingying, Vatapalli, Rajita, Hennessey, Patrick T., Ahn, Julie, Danilova, Ludmila V., Khan, Zubair, Bishop, Justin A., Koch, Wayne M., Westra, William H., Ochs, Michael F., Califano, Joseph A.
Published in Cancer research (Chicago, Ill.) (01.08.2015)
Published in Cancer research (Chicago, Ill.) (01.08.2015)
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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
Fertig, Elana J., Markovic, Ana, Danilova, Ludmila V., Gaykalova, Daria A., Cope, Leslie, Chung, Christine H., Califano, Joseph A., Ochs, Michael F.
Published in Cancer research (Chicago, Ill.) (15.04.2013)
Published in Cancer research (Chicago, Ill.) (15.04.2013)
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Journal Article
Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway Analysis: e78127
Fertig, Elana J, Markovic, Ana, Danilova, Ludmila V, Gaykalova, Daria A, Cope, Leslie, Chung, Christine H, Ochs, Michael F, Califano, Joseph A
Published in PloS one (01.11.2013)
Published in PloS one (01.11.2013)
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