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Daria A. Gaykalova · SciRah

Researcher profile · Semantic Scholar

Daria A. Gaykalova

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Daria A. Gaykalova — researcher profile on SciRah

h-index: 31
Works: 99
Citations: 2,739

Most-cited papers

Nucleosomes can form a polar barrier to transcript elongation by RNA polymerase II.
V. Bondarenko, L. M. Steele, A. Újvári, Daria A. Gaykalova +4 more
2006Molecules and Cells280 citations
Semantic Scholar
Activation of the NOTCH pathway in Head and Neck Cancer
Wenyue Sun, Daria A. Gaykalova, M. Ochs, E. Mambo +22 more
2013Cancer Research206 citations Open access
Semantic Scholar
Mechanism of chromatin remodeling and recovery during passage of RNA polymerase II
O. I. Kulaeva, Daria A. Gaykalova, N. Pestov, Viktor V. Golovastov +3 more
2009Nature Structural &Molecular Biology187 citations Open access
Semantic Scholar
Using DNA mechanics to predict in vitro nucleosome positions and formation energies
A. Morozov, Karissa Fortney, Daria A. Gaykalova, V. Studitsky +2 more
2009Nucleic Acids Research179 citations Open access
Semantic Scholar
Epigenetic regulation of gene expression in cancer: techniques, resources and analysis
L. Kagohara, G. Stein-O'Brien, Dylan Kelley, Emily Flam +7 more
2017bioRxiv112 citations Open access
Semantic Scholar
Transcription through chromatin by RNA polymerase II: histone displacement and exchange.
O. I. Kulaeva, Daria A. Gaykalova, V. Studitsky
2007Mutation research98 citations Open access
Semantic Scholar
HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers
Shu-Ling Ren, Daria A. Gaykalova, Theresa Guo, Alexander V. Favorov +19 more
2020Oncogene93 citations Open access
Semantic Scholar
Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma
Daria A. Gaykalova, E. Mambo, A. Choudhary, Jeffery Houghton +15 more
2014PLoS ONE87 citations Open access
Semantic Scholar
Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers
Mizuo Ando, Y. Saito, Guo-Rong Xu, N. Bui +21 more
2019Nature Communications86 citations Open access
Semantic Scholar
Structural analysis of nucleosomal barrier to transcription
Daria A. Gaykalova, O. I. Kulaeva, O. Volokh, A. Shaytan +4 more
2015Proceedings of the National Academy of Sciences of the United States of America73 citations Open access
Semantic Scholar
Molecular mechanisms of human papillomavirus-related carcinogenesis in head and neck cancer
F. Faraji, Munfarid A. Zaidi, C. Fakhry, Daria A. Gaykalova
2017bioRxiv69 citations Open access
Semantic Scholar
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF
G. Stein-O'Brien, J. Carey, Wai-Shing Lee, M. Considine +12 more
2016bioRxiv53 citations Open access
Semantic Scholar
BORIS binding to the promoters of cancer testis antigens, MAGEA2, MAGEA3 and MAGEA4, is associated with their transcriptional activation in lung cancer
Sheetal Bhan, Sandeep S. Negi, Chunbo Shao, Chad A. Glazer +6 more
2011Clinical Cancer Research53 citations Open access
Semantic Scholar
Entinostat in combination with nivolumab in metastatic pancreatic ductal adenocarcinoma: a phase 2 clinical trial
M. Baretti, Ludmila Danilova, J. Durham, Courtney B. Betts +20 more
2024Nature Communications52 citations Open access
Semantic Scholar
NF-κB and STAT3 Transcription Factor Signatures Differentiate HPV-positive and HPV-negative Head and Neck Squamous Cell Carcinoma
Daria A. Gaykalova, J. Manola, Hiroyuki Ozawa, V. Žižková +16 more
2015International Journal of Cancer52 citations Open access
Semantic Scholar
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
Dylan Kelley, Emily Flam, E. Izumchenko, L. Danilova +18 more
2017Cancer Research51 citations Open access
Semantic Scholar
Entinostat decreases immune suppression to promote anti-tumor responses in a HER2+ breast tumor microenvironment
Dimitri N. Sidiropoulos, C. Rafie, J. Jang, Sofi Castanon +22 more
2022Cancer immunology research50 citations Open access
Semantic Scholar
Preparation and Analysis of Uniquely Positioned Mononucleosomes
Daria A. Gaykalova, O. I. Kulaeva, V. Bondarenko, V. Studitsky
2009Methods in molecular biology50 citations Open access
Semantic Scholar
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, M. Considine +12 more
2017Cancer Research43 citations Open access
Semantic Scholar
Serum antibodies to HPV16 early proteins as biomarkers for risk stratification and recurrence of HPV-associated oropharyngeal cancer
C. Fakhry, J. Qualliotine, Zhe Zhang, N. Agrawal +8 more
2015Cancer Prevention Research43 citations Open access
Semantic Scholar
Discovery and development of differentially methylated regions in human papillomavirus‐related oropharyngeal squamous cell carcinoma
Shu-Ling Ren, Daria A. Gaykalova, J. Wang, Theresa Guo +15 more
2018International Journal of Cancer42 citations Open access
Semantic Scholar
Preferential Activation of the Hedgehog Pathway by Epigenetic Modulations in HPV Negative HNSCC Identified with Meta-Pathway Analysis
E. Fertig, Ana Marković, L. Danilova, Daria A. Gaykalova +4 more
2013PLoS ONE41 citations Open access
Semantic Scholar
The use of machine learning to discover regulatory networks controlling biological systems
Rossin Erbe, Jessica Gore, K. Gemmill, Daria A. Gaykalova +1 more
2022Molecules and Cells39 citations Open access
Semantic Scholar
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 lines
L. Kagohara, Fernando T. Zamuner, Emily F. Davis-Marcisak, Gaurav Sharma +5 more
2020British Journal of Cancer38 citations Open access
Semantic Scholar
Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients
Daria A. Gaykalova, Rajita Vatapalli, Ying-Ying Wei, Hua-Ling Tsai +15 more
2015PLoS ONE38 citations Open access
Semantic Scholar
Suprabasin Is Hypomethylated and Associated with Metastasis in Salivary Adenoid Cystic Carcinoma
Chunbo Shao, M. Tan, J. Bishop, Jia Liu +11 more
2012PLoS ONE36 citations Open access
Semantic Scholar
A polar barrier to transcription can be circumvented by remodeler-induced nucleosome translocation
Daria A. Gaykalova, V. Nagarajavel, V. Bondarenko, Blaine Bartholomew +2 more
2011Nucleic Acids Research36 citations Open access
Semantic Scholar
Expression Microarray Analysis Reveals Alternative Splicing of LAMA3 and DST Genes in Head and Neck Squamous Cell Carcinoma
Ryan J. Li, M. Ochs, S. Ahn, P. Hennessey +10 more
2014PLoS ONE35 citations Open access
Semantic Scholar
PDGF enhances the protective effect of adipose stem cell-derived extracellular vesicles in a model of acute hindlimb ischemia
T. Lopatina, E. Favaro, C. Grange, M. Cedrino +8 more
2018Scientific Reports34 citations Open access
Semantic Scholar
Dose-Dependent Activation of Putative Oncogene SBSN by BORIS
Daria A. Gaykalova, Rajita Vatapalli, Chad A. Glazer, Sheetal Bhan +4 more
2012PLoS ONE32 citations Open access
Semantic Scholar
Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance
G. Stein-O'Brien, L. Kagohara, Si-Jia Li, Manjusha Thakar +12 more
2018Genome Medicine31 citations Open access
Semantic Scholar
In silico analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia
Eugene Makarev, A. Schubert, Riya R. Kanherkar, N. London +13 more
2017Cell Death Discovery31 citations Open access
Semantic Scholar
Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma
Theresa Guo, Kristina D. Zambo, Fernando T. Zamuner, Tingting Ou +12 more
2020Epigenetics29 citations Open access
Semantic Scholar
Expression of programmed cell death-ligand 1 and associated lymphocyte infiltration in olfactory neuroblastoma.
N. London, L. Rooper, J. Bishop, Haiying Xu +7 more
2019World Neurosurgery27 citations
Semantic Scholar
Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma
A. Schubert, Esther Channah Broner, N. Agrawal, N. London +15 more
2019Cancer Letters24 citations Open access
Semantic Scholar
DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma
A. Finegersh, S. Kulich, Theresa Guo, Alexander V. Favorov +5 more
2017Scientific Reports23 citations Open access
Semantic Scholar
Extracellular Vesicles Released by Tumor Endothelial Cells Spread Immunosuppressive and Transforming Signals Through Various Recipient Cells
T. Lopatina, E. Favaro, L. Danilova, E. Fertig +10 more
2020Frontiers in Cell and Developmental Biology22 citations Open access
Semantic Scholar
Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC
Daria A. Gaykalova, V. Žižková, Theresa Guo, Ilse Tiscareno +13 more
2017OncoTarget21 citations Open access
Semantic Scholar
Epigenetic Regulations of Perineural Invasion in Head and Neck Squamous Cell Carcinoma
P. Hurník, Z. Chyra, T. Ševčíková, J. Štembírek +4 more
2022Frontiers in Genetics18 citations Open access
Semantic Scholar
Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor
Hitendra S. Solanki, R. Raja, A. Zhavoronkov, I. Ozerov +21 more
2018Oncoscience18 citations Open access
Semantic Scholar
Experimental analysis of the mechanism of chromatin remodeling by RNA polymerase II
Daria A. Gaykalova, O. I. Kulaeva, N. Pestov, F. Hsieh +1 more
2012Methods in Enzymology18 citations Open access
Semantic Scholar
CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network
E. Fertig, Hiroyuki Ozawa, Manjusha Thakar, J. Howard +12 more
2016OncoTarget15 citations Open access
Semantic Scholar
Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer
Emily Flam, L. Danilova, Dylan Kelley, E. Stavrovskaya +7 more
2019Scientific Reports14 citations Open access
Semantic Scholar
HEY1 is expressed independent of NOTCH1 and is associated with poor prognosis in head and neck squamous cell carcinoma.
E. Rettig, J. Bishop, N. Agrawal, C. Chung +8 more
2018Oral Oncology13 citations
Semantic Scholar
Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma.
Dylan Kelley, Emily Flam, Theresa Guo, L. Danilova +16 more
2018Translational Research: The Journal of Laboratory and Clinical Medicine13 citations Open access
Semantic Scholar
Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination
J. Stansfield, Matthew Rusay, Roger Shan, Conor J. Kelton +4 more
2016Cancer Informatics11 citations Open access
Semantic Scholar
SpliceMutr Enables Pan-Cancer Analysis of Splicing-Derived Neoantigen Burden in Tumors
T. Palmer, Michael D. Kessler, X. Shao, A. Balan +13 more
2023bioRxiv10 citations Open access
Semantic Scholar
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 lines
L. T. Kagohara, Fernando T. Zamuner, M. Considine, J. Allen +3 more
2019bioRxiv10 citations Open access
Semantic Scholar
Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID
Alexey K. Shaytan, Hua Xiao, G. Armeev, Daria A. Gaykalova +5 more
2018Nature Protocols10 citations Open access
Semantic Scholar
Splice Expression Variation Analysis (SEVA) for Inter-tumor Heterogeneity of Gene Isoform Usage in Cancer
Bahman Afsari, Theresa Guo, M. Considine, Liliana D. Florea +12 more
2016bioRxiv10 citations Open access
Semantic Scholar

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