Molecular mechanisms of human papillomavirus-related carcinogenesis in head and neck cancer

von Faraji, Farhoud, Zaidi, Munfarid, Fakhry, Carole, Gaykalova, Daria A.
Veröffentlicht in Microbes Infect (2017)

Preparation and Analysis of Uniquely Positioned Mononucleosomes

von Gaykalova, Daria A., Kulaeva, Olga I., Bondarenko, Vladimir A., Studitsky, Vasily M.
Veröffentlicht in Methods Mol Biol (2009)

Correcting Transcription Factor Gene Sets for Copy Number and Promoter Methylation Variations

von Rathi, Komal S., Gaykalova, Daria A., Hennesey, Patrick, Califano, Joseph A., Ochs, Michael F.
Veröffentlicht 2014

Experimental analysis of the mechanism of chromatin remodeling by RNA polymerase II

von Gaykalova, Daria A., Kulaeva, Olga I., Pestov, Nikolai A., Hsieh, Fu-Kai, Studitsky, Vasily M.
Veröffentlicht 2012

Using DNA mechanics to predict in vitro nucleosome positions and formation energies

von Morozov, Alexandre V., Fortney, Karissa, Gaykalova, Daria A., Studitsky, Vasily M., Widom, Jonathan, Siggia, Eric D.
Veröffentlicht 2009

A polar barrier to transcription can be circumvented by remodeler-induced nucleosome translocation

von Gaykalova, Daria A., Nagarajavel, V., Bondarenko, Vladimir A., Bartholomew, Blaine, Clark, David J., Studitsky, Vasily M.
Veröffentlicht 2011

Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets

von Erbe, Rossin, Kessler, Michael D, Favorov, Alexander V, Easwaran, Hariharan, Gaykalova, Daria A, Fertig, Elana J
Veröffentlicht in Nucleic Acids Res (2020)

Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II

von Kulaeva, Olga I., Gaykalova, Daria A., Pestov, Nikolai A., Golovastov, Viktor V., Vassylyev, Dmitry G., Artsimovitch, Irina, Studitsky, Vasily M.
Veröffentlicht 2009

Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination

von Stansfield, John C., Rusay, Matthew, Shan, Roger, Kelton, Conor, Gaykalova, Daria A., Fertig, Elana J., Califano, Joseph A., Ochs, Michael F.
Veröffentlicht in Cancer Inform (2016)

Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway Analysis

von Fertig, Elana J., Markovic, Ana, Danilova, Ludmila V., Gaykalova, Daria A., Cope, Leslie, Chung, Christine H., Ochs, Michael F., Califano, Joseph A.
Veröffentlicht 2013

Structural analysis of nucleosomal barrier to transcription

von Gaykalova, Daria A., Kulaeva, Olga I., Volokh, Olesya, Shaytan, Alexey K., Hsieh, Fu-Kai, Kirpichnikov, Mikhail P., Sokolova, Olga S., Studitsky, Vasily M.
Veröffentlicht in Proc Natl Acad Sci U S A (2015)

Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensitive cell lin...

von Kagohara, Luciane T., Zamuner, Fernando, Davis-Marcisak, Emily F., Sharma, Gaurav, Considine, Michael, Allen, Jawara, Yegnasubramanian, Srinivasan, Gaykalova, Daria A., Fertig, Elana J.
Veröffentlicht in Br J Cancer (2020)

Correction: Integrated single-cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC-sensit...

von Kagohara, Luciane T., Zamuner, Fernando, Davis-Marcisak, Emily F., Sharma, Gaurav, Considine, Michael, Allen, Jawara, Yegnasubramanian, Srinivasan, Gaykalova, Daria A., Fertig, Elana J.
Veröffentlicht in Br J Cancer (2020)

DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma

von Finegersh, Andrey, Kulich, Scott, Guo, Theresa, Favorov, Alexander V., Fertig, Elana J., Danilova, Ludmila V., Gaykalova, Daria A., Califano, Joseph A., Duvvuri, Umamaheswar
Veröffentlicht in Sci Rep (2017)

BORIS binding to the promoters of cancer testis antigens, MAGEA2, MAGEA3 and MAGEA4, is associated with their transcriptional activation in lung cancer

von Bhan, Sheetal, Negi, Sandeep S., Shao, Chunbo, Glazer, Chad A., Chuang, Alice, Gaykalova, Daria A., Sun, Wenyue, Sidransky, David, Ha, Patrick K., Califano, Joseph A.
Veröffentlicht 2011

Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID

von Shaytan, Alexey K., Xiao, Hua, Armeev, Grigoriy A., Gaykalova, Daria A., Komarova, Galina A., Wu, Carl, Studitsky, Vasily M., Landsman, David, Panchenko, Anna R.
Veröffentlicht in Nat Protoc (2018)

PDGF enhances the protective effect of adipose stem cell-derived extracellular vesicles in a model of acute hindlimb ischemia

von Lopatina, Tatiana, Favaro, Enrica, Grange, Cristina, Cedrino, Massimo, Ranghino, Andrea, Occhipinti, Sergio, Fallo, Sofia, Buffolo, Fabrizio, Gaykalova, Daria A., Zanone, Maria M., Romagnoli, Renato, Camussi, Giovanni
Veröffentlicht in Sci Rep (2018)

Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer

von Flam, Emily L., Danilova, Ludmila, Kelley, Dylan Z., Stavrovskaya, Elena, Guo, Theresa, Considine, Michael, Qian, Jiang, Califano, Joseph A., Favorov, Alexander, Fertig, Elana J., Gaykalova, Daria A.
Veröffentlicht in Sci Rep (2019)

Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma

von Guo, Theresa, Gaykalova, Daria A., Considine, Michael, Wheelan, Sarah, Pallavajjala, Aparna, Bishop, Justin A, Westra, William H., Ideker, Trey, Koch, Wayne M, Khan, Zubair, Fertig, Elana J., Califano, Joseph A.
Veröffentlicht in Int J Cancer (2016)

Epigenetic regulation of gene expression in cancer: techniques, resources and analysis

von 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
Veröffentlicht in Brief Funct Genomics (2017)