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

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

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

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

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

por Erbe, Rossin, Kessler, Michael D, Favorov, Alexander V, Easwaran, Hariharan, Gaykalova, Daria A, Fertig, Elana J
Publicado 2020

Identification of CT-based non-invasive Radiographic Biomarkers for Overall Survival Stratification in Oral Cavity Squamous Cell Carcinoma

por Ling, Xiao, Alexander, Gregory S., Molitoris, Jason, Choi, Jinhyuk, Schumaker, Lisa, Mehra, Ranee, Gaykalova, Daria A., Ren, Lei
Publicado 2023

Epigenetic Regulations of Perineural Invasion in Head and Neck Squamous Cell Carcinoma

por Hurník, Pavel, Chyra, Zuzana, Ševčíková, Tereza, Štembírek, Jan, Trtková, Kateřina Smešný, Gaykalova, Daria A., Buchtová, Marcela, Hrubá, Eva
Publicado 2022

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

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

Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination

por Stansfield, John C., Rusay, Matthew, Shan, Roger, Kelton, Conor, Gaykalova, Daria A., Fertig, Elana J., Califano, Joseph A., Ochs, Michael F.
Publicado 2016

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

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

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...

por Kagohara, Luciane T., Zamuner, Fernando, Davis-Marcisak, Emily F., Sharma, Gaurav, Considine, Michael, Allen, Jawara, Yegnasubramanian, Srinivasan, Gaykalova, Daria A., Fertig, Elana J.
Publicado 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...

por Kagohara, Luciane T., Zamuner, Fernando, Davis-Marcisak, Emily F., Sharma, Gaurav, Considine, Michael, Allen, Jawara, Yegnasubramanian, Srinivasan, Gaykalova, Daria A., Fertig, Elana J.
Publicado 2020

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

por Finegersh, Andrey, Kulich, Scott, Guo, Theresa, Favorov, Alexander V., Fertig, Elana J., Danilova, Ludmila V., Gaykalova, Daria A., Califano, Joseph A., Duvvuri, Umamaheswar
Publicado 2017

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

por 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
Publicado 2018

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

por 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.
Publicado 2019

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

por 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
Publicado 2017

Extracellular Vesicles Released by Tumor Endothelial Cells Spread Immunosuppressive and Transforming Signals Through Various Recipient Cells

por Lopatina, Tatiana, Favaro, Enrica, Danilova, Ludmila, Fertig, Elana J., Favorov, Alexander V., Kagohara, Luciane T., Martone, Tiziana, Bussolati, Benedetta, Romagnoli, Renato, Albera, Roberto, Pecorari, Giancarlo, Brizzi, Maria Felice, Camussi, Giovanni, Gaykalova, Daria A.
Publicado 2020

Expression Microarray Analysis Reveals Alternative Splicing of LAMA3 and DST Genes in Head and Neck Squamous Cell Carcinoma

por Li, Ryan, Ochs, Michael F., Ahn, Sun Mi, Hennessey, Patrick, Tan, Marietta, Soudry, Ethan, Gaykalova, Daria A., Uemura, Mamoru, Brait, Mariana, Shao, Chunbo, Westra, William, Bishop, Justin, Fertig, Elana J., Califano, Joseph A.
Publicado 2014

Suprabasin Is Hypomethylated and Associated with Metastasis in Salivary Adenoid Cystic Carcinoma

por Shao, Chunbo, Tan, Marietta, Bishop, Justin A., Liu, Jia, Bai, Weiliang, Gaykalova, Daria A., Ogawa, Takenori, Vikani, Ami R., Agrawal, Yuri, Li, Ryan J., Kim, Myoung Sook, Westra, William H., Sidransky, David, Califano, Joseph A., Ha, Patrick K.
Publicado 2012

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer

por Sherman, Thomas D., Kagohara, Luciane T., Cao, Raymon, Cheng, Raymond, Satriano, Matthew, Considine, Michael, Krigsfeld, Gabriel, Ranaweera, Ruchira, Tang, Yong, Jablonski, Sandra A., Stein-O'Brien, Genevieve, Gaykalova, Daria A., Weiner, Louis M., Chung, Christine H., Fertig, Elana J.
Publicado 2019

In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia

por Makarev, Eugene, Schubert, Adrian D, Kanherkar, Riya R, London, Nyall, Teka, Mahder, Ozerov, Ivan, Lezhnina, Ksenia, Bedi, Atul, Ravi, Rajani, Mehra, Rannee, Hoque, Mohammad O, Sloma, Ido, Gaykalova, Daria A, Csoka, Antonei B, Sidransky, David, Zhavoronkov, Alex, Izumchenko, Evgeny
Publicado 2017

CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network

por Fertig, Elana J., Ozawa, Hiroyuki, Thakar, Manjusha, Howard, Jason D., Kagohara, Luciane T., Krigsfeld, Gabriel, Ranaweera, Ruchira S., Hughes, Robert M., Perez, Jimena, Jones, Siân, Favorov, Alexander V., Carey, Jacob, Stein-O'Brien, Genevieve, Gaykalova, Daria A., Ochs, Michael F., Chung, Christine H.
Publicado 2016