Daria Gaykalova

Assistant Professor

20062019
If you made any changes in Pure, your changes will be visible here soon.

Research Output 2006 2019

2019

Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers

Ando, M., Saito, Y., Xu, G., Bui, N. Q., Medetgul-Ernar, K., Pu, M., Fisch, K., Ren, S., Sakai, A., Fukusumi, T., Liu, C., Haft, S., Pang, J., Mark, A., Gaykalova, D., Guo, T., Favorov, A., Yegnasubramanian, S., Fertig, E., Ha, P. & 5 others, Tamayo, P., Yamasoba, T., Ideker, T., Messer, K. & Califano, J. A., Dec 1 2019, In : Nature communications. 10, 1, 2188.

Research output: Contribution to journalArticle

Open Access
chromatin
methylation
Transcription Initiation Site
DNA Methylation
Chromatin

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

Flam, E. L., Danilova, L., Kelley, D. Z., Stavrovskaya, E., Guo, T., Considine, M., Qian, J., Califano, J. A., Favorov, A., Fertig, E. J. & Gaykalova, D. A., Dec 1 2019, In : Scientific reports. 9, 1, 15034.

Research output: Contribution to journalArticle

Open Access
Gene Expression
Neoplasms
Chromatin
Genes
DNA Methylation

Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers (Nature Communications, (2019), 10, 1, (2188), 10.1038/s41467-019-09937-w)

Ando, M., Saito, Y., Xu, G., Bui, N. Q., Medetgul-Ernar, K., Pu, M., Fisch, K., Ren, S., Sakai, A., Fukusumi, T., Liu, C., Haft, S., Pang, J., Mark, A., Gaykalova, D., Guo, T., Favorov, A., Yegnasubramanian, S., Fertig, E., Ha, P. & 5 others, Tamayo, P., Yamasoba, T., Ideker, T., Messer, K. & Califano, J. A., Dec 1 2019, In : Nature communications. 10, 1, 2415.

Research output: Contribution to journalComment/debate

Open Access
chromatin
methylation
Transcription Initiation Site
DNA Methylation
medicine
2018

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

Sherman, T. D., Tsukamoto Kagohara, L., Cao, R., Cheng, R., Satriano, M., Considine, M., Krigsfeld, G., Ranaweera, R., Tang, Y., Jablonski, S. A., Stein-O'Brien, G., Gaykalova, D., Weiner, L. M., Chung, C. H. & Fertig, E., Jun 1 2018, In : PLoS computational biology. 14, 4, p. e1006935

Research output: Contribution to journalArticle

Open Access
Statistical Modeling
Bioinformatics
Gene Expression Data
Gene expression
Mathematical Modeling

Discovery and development of differentially methylated regions in human papillomavirus-related oropharyngeal squamous cell carcinoma

Ren, S., Gaykalova, D., Wang, J., Guo, T., Danilova, L. V., Favorov, A., Fertig, E., Bishop, J., Khan, Z., Flam, E., Wysocki, P. T., DeJong, P., Ando, M., Liu, C., Sakai, A., Fukusumi, T., Haft, S., Sadat, S. & Califano, J. A., Jan 1 2018, (Accepted/In press) In : International Journal of Cancer.

Research output: Contribution to journalArticle

Squamous Cell Carcinoma
Methylation
DNA Methylation
Genome
Atlases

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

Tsukamoto Kagohara, L., Stein-O'Brien, G. L., Kelley, D., Flam, E., Wick, H. C., Danilova, L. V., Easwaran, H., Favorov, A., Qian, J., Gaykalova, D. & Fertig, E., Jan 1 2018, In : Briefings in Functional Genomics. 17, 1, p. 49-63 15 p.

Research output: Contribution to journalReview article

Gene Expression Regulation
Bioinformatics
Epigenomics
Gene expression
Throughput

Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma

Kelley, D. Z., Flam, E. L., Guo, T., Danilova, L. V., Zamuner, F. T., Bohrson, C., Considine, M., Windsor, E. J., Bishop, J. A., Zhang, C., Koch, W. M., Sidransky, D., Westra, W. H., Chung, C. H., Califano, J. A., Wheelan, S., Favorov, A., Florea, L. D., Fertig, E. & Gaykalova, D., Jan 1 2018, (Accepted/In press) In : Translational Research.

Research output: Contribution to journalArticle

Alternative Splicing
Protein Isoforms
Tumors
Neoplasms
Cell proliferation

HEY1 is expressed independent of NOTCH1 and is associated with poor prognosis in head and neck squamous cell carcinoma

Rettig, E. M., Bishop, J. A., Agrawal, N., Chung, C. H., Sharma, R., Zamuner, F., Li, R. J., Koch, W. M., Califano, J. A., Guo, T., Gaykalova, D. & Fakhry, C., Jul 1 2018, In : Oral Oncology. 82, p. 168-175 8 p.

Research output: Contribution to journalArticle

Mutation
Neoplasms
Proportional Hazards Models
Carcinoma, squamous cell of head and neck
Staining and Labeling

Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance

Stein-O'Brien, G., Tsukamoto Kagohara, L., Li, S., Thakar, M., Ranaweera, R., Ozawa, H., Cheng, H., Considine, M., Schmitz, S., Favorov, A., Danilova, L. V., Califano, J. A., Izumchenko, E., Gaykalova, D., Chung, C. H. & Fertig, E., May 23 2018, In : Genome Medicine. 10, 1, 37.

Research output: Contribution to journalArticle

Epigenomics
DNA Methylation
Molecular Dynamics Simulation
RNA Sequence Analysis
Phenotype

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

Lopatina, T., Favaro, E., Grange, C., Cedrino, M., Ranghino, A., Occhipinti, S., Fallo, S., Buffolo, F., Gaykalova, D., Zanone, M. M., Romagnoli, R. & Camussi, G., Dec 1 2018, In : Scientific Reports. 8, 1, 17458.

Research output: Contribution to journalArticle

Platelet-Derived Growth Factor
Hindlimb
Stem Cells
Ischemia
Blood Cells

Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer

Afsari, B., Guo, T., Considine, M., Florea, L. D., Tsukamoto Kagohara, L., Stein-O'Brien, G. L., Kelley, D., Flam, E., Zambo, K. D., Ha, P. K., Geman, D., Ochs, M. F., Califano, J. A., Gaykalova, D., Favorov, A. & Fertig, E., Jun 1 2018, In : Bioinformatics. 34, 11, p. 1859-1867 9 p.

Research output: Contribution to journalArticle

Tumors
Tumor
Cancer
Protein Isoforms
Genes

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

Shaytan, A. K., Xiao, H., Armeev, G. A., Gaykalova, D., Komarova, G. A., Wu, C., Studitsky, V. M., Landsman, D. & Panchenko, A. R., Jan 1 2018, (Accepted/In press) In : Nature Protocols.

Research output: Contribution to journalArticle

DNA Footprinting
Hydroxyl Radical
DNA
Experiments
Structural Models
2017

A novel functional splice variant of AKT3 defined by analysis of alternative splice expression in HPV-positive oropharyngeal cancers

Guo, T., Sakai, A., Afsari, B., Considine, M., Danilova, L. V., Favorov, A., Yegnasubramanian, S., Kelley, D. Z., Flam, E., Ha, P. K., Khan, Z., Wheelan, S., Gutkind, J. S., Fertig, E., Gaykalova, D. & Califano, J., Oct 1 2017, In : Cancer Research. 77, 19, p. 5248-5258 11 p.

Research output: Contribution to journalArticle

Oropharyngeal Neoplasms
Alternative Splicing
Methylation
RNA Sequence Analysis
Squamous Cell Carcinoma

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

Finegersh, A., Kulich, S., Guo, T., Favorov, A., Fertig, E., Danilova, L. V., Gaykalova, D., Califano, J. A. & Duvvuri, U., Dec 1 2017, In : Scientific Reports. 7, 1, 15173.

Research output: Contribution to journalArticle

CpG Islands
DNA Methylation
Keratinocytes
Methylation
Chloride Channels

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, D. Z., Flam, E. L., Izumchenko, E., Danilova, L. V., Wulf, H. A., Guo, T., Singman, D. A., Afsari, B., Skaist, A. M., Considine, M., Welch, J. A., Stavrovskaya, E., Bishop, J. A., Westra, W. H., Khan, Z., Koch, W. M., Sidransky, D., Wheelan, S., Califano, J. A., Favorov, A. & 2 others, Fertig, E. & Gaykalova, D., Dec 1 2017, In : Cancer Research. 77, 23, p. 6538-6550 13 p.

Research output: Contribution to journalArticle

RNA Sequence Analysis
Chromatin Immunoprecipitation
Chromatin
Neck
Head

Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC

Gaykalova, D., Zizkova, V., Guo, T., Tiscareno, I., Wei, Y., Vatapalli, R., Hennessey, P. T., Ahn, J., Danilova, L. V., Khan, Z., Bishop, J. A., Silvio Gutkind, J., Koch, W. M., Westra, W. H., Fertig, E., Ochs, M. F. & Califano, J. A., 2017, In : Oncotarget. 8, 9, p. 15349-15363 15 p.

Research output: Contribution to journalArticle

Tumor Suppressor Genes
Epigenomics
Methylation
Neoplasms
Genome

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

Faraji, F., Zaidi, M., Fakhry, C. & Gaykalova, D., 2017, (Accepted/In press) In : Microbes and Infection.

Research output: Contribution to journalArticle

Head and Neck Neoplasms
Carcinogenesis
Squamous Cell Carcinoma
Genome
Carcinoma, squamous cell of head and neck

PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF

Stein-O'Brien, G. L., Carey, J. L., Lee, W. S., Considine, M., Favorov, A., Flam, E., Guo, T., Li, S., Marchionni, L., Sherman, T., Sivy, S., Gaykalova, D., McKay, R. D., Ochs, M. F., Colantuoni, C. & Fertig, E., Jun 15 2017, In : Bioinformatics. 33, 12, p. 1892-1894 3 p.

Research output: Contribution to journalArticle

Matrix Factorization
Biomarkers
Factorization
Transcriptome
Data-driven
2016

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

Guo, T., Gaykalova, D., Considine, M., Wheelan, S., Pallavajjalla, A., Bishop, J. A., Westra, W. H., Ideker, T., Koch, W. M., Khan, Z., Fertig, E. & Califano, J. A., 2016, (Accepted/In press) In : International Journal of Cancer.

Research output: Contribution to journalArticle

Gene Fusion
Squamous Cell Carcinoma
Neoplasms
Up-Regulation
Down-Regulation

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

Fertig, E., Ozawa, H., Thakar, M., Howard, J. D., Tsukamoto Kagohara, L., Krigsfeld, G., Ranaweera, R. S., Hughes, R. M., Perez, J., Jones, S., Favorov, A., Carey, J., Stein-O'Brien, G., Gaykalova, D., Ochs, M. F. & Chung, C. H., 2016, In : Oncotarget. 7, 45, p. 73845-73864 20 p.

Research output: Contribution to journalArticle

Transcription Factor AP-2
Phosphatidylinositol 3-Kinases
Transcriptome
Genes
Neoplasms

Serum antibodies to HPV16 early proteins warrant investigation as potential biomarkers for risk stratification and recurrence of hpv-associated oropharyngeal cancer

Fakhry, C., Qualliotine, J. R., Zhang, Z., Agrawal, N., Gaykalova, D., Bishop, J. A., Subramaniam, R. M., Koch, W. M., Chung, C. H., Eisele, D. W., Califano, J. & Viscidi, R. P., Feb 1 2016, In : Cancer Prevention Research. 9, 2, p. 135-141 7 p.

Research output: Contribution to journalArticle

Oropharyngeal Neoplasms
Biomarkers
Recurrence
Antibodies
Serum
2015

NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma

Gaykalova, D., Manola, J. B., Ozawa, H., Zizkova, V., Morton, K., Bishop, J. A., Sharma, R., Zhang, C., Michailidi, C., Considine, M., Tan, M., Fertig, E., Hennessey, P. T., Ahn, J., Koch, W. M., Westra, W. H., Khan, Z., Chung, C. H., Ochs, M. F. & Califano, J. A., Oct 15 2015, In : International Journal of Cancer. 137, 8, p. 1879-1889 11 p.

Research output: Contribution to journalArticle

Transcription Factors
Biomarkers
Carcinoma, squamous cell of head and neck
Loss of Heterozygosity
Gene Silencing

Outlier analysis defines zinc finger gene family DNA methylation in tumors and saliva of head and neck cancer patients

Gaykalova, D., Vatapalli, R., Wei, Y., Tsai, H. L., Wang, H., Zhang, C., Hennessey, P. T., Guo, T., Tan, M., Li, R., Ahn, J., Khan, Z., Westra, W. H., Bishop, J. A., Zaboli, D., Koch, W. M., Khan, T., Ochs, M. F. & Califano, J. A., Nov 6 2015, In : PLoS One. 10, 11, e0142148.

Research output: Contribution to journalArticle

zinc finger motif
Zinc Fingers
squamous cell carcinoma
DNA methylation
DNA Methylation

Structural analysis of nucleosomal barrier to transcription

Gaykalova, D., Kulaeva, O. I., Volokh, O., Shaytan, A. K., Hsieh, F. K., Kirpichnikov, M. P., Sokolova, O. S. & Studitsky, V. M., Oct 27 2015, In : Proceedings of the National Academy of Sciences of the United States of America. 112, 43, p. E5787-E5795

Research output: Contribution to journalArticle

Nucleosomes
Histones
DNA
Proteins
RNA Polymerase II

Toward signaling-driven biomarkers immune to normal tissue contamination

Stansfield, J. C., Rusay, M., Shan, R., Kelton, C., Gaykalova, D., Fertig, E., Califano, J. A. & Ochs, M. F., Dec 10 2015, In : Cancer Informatics. 15, p. 15-21 7 p.

Research output: Contribution to journalArticle

Biomarkers
Natural Language Processing
Genes
Neoplasms
Atlases
2014

Activation of the NOTCH pathway in head and neck cancer

Sun, W., Gaykalova, D., Ochs, M. F., Mambo, E., Arnaoutakis, D., Liu, Y., Loyo, M., Agrawal, N., Howard, J., Li, R., Ahn, S., Fertig, E., Sidransky, D., Houghton, J., Buddavarapu, K., Sanford, T., Choudhary, A., Darden, W., Adai, A., Latham, G. & 6 others, Bishop, J., Sharma, R., Westra, W. H., Hennessey, P., Chung, C. H. & Califano, J. A., Feb 15 2014, In : Cancer Research. 74, 4, p. 1091-1104 14 p.

Research output: Contribution to journalArticle

Head and Neck Neoplasms
Mutation
Ligands
Genes
Neoplasms

Correcting transcription factor gene sets for copy number and promoter methylation variations

Rathi, K. S., Gaykalova, D., Hennessey, P., Califano, J. A. & Ochs, M. F., 2014, In : Drug Development Research. 75, 6, p. 343-347 5 p.

Research output: Contribution to journalArticle

Gene Dosage
Methylation
Transcription Factors
Genes
Gene Silencing

Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma

Li, R., Ochs, M. F., Ahn, S. M., Hennessey, P., Tan, M., Soudry, E., Gaykalova, D., Uemura, M., Brait Rodrigues De Oliveira, M., Shao, C., Westra, W., Bishop, J., Fertig, E. & Califano, J. A., Mar 27 2014, In : PLoS One. 9, 3, e91263.

Research output: Contribution to journalArticle

alternative splicing
squamous cell carcinoma
Alternative Splicing
Microarray Analysis
Microarrays

Novel insight into mutational landscape of head and neck squamous cell carcinoma

Gaykalova, D., Mambo, E., Choudhary, A., Houghton, J., Buddavarapu, K., Sanford, T., Darden, W., Adai, A., Hadd, A., Latham, G., Danilova, L. V., Bishop, J., Li, R. J., Westra, W. H., Hennessey, P., Koch, W. M., Ochs, M. F., Califano, J. A. & Sun, W., Mar 25 2014, In : PLoS One. 9, 3, e93102.

Research output: Contribution to journalArticle

squamous cell carcinoma
neck
mutation
Mutation
Genes
2013

Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis

Fertig, E., Markovic, A., Danilova, L. V., Gaykalova, D., Cope, L., Chung, C. H., Ochs, M. F. & Califano, J. A., Nov 4 2013, In : PLoS One. 8, 11, e78127.

Research output: Contribution to journalArticle

Erinaceidae
Papillomaviridae
squamous cell carcinoma
Epigenomics
epigenetics
2012

Dose-dependent activation of putative oncogene SBSN by BORIS

Gaykalova, D., Vatapalli, R., Glazer, C. A., Bhan, S., Shao, C., Sidransky, D., Ha, P. K. & Califano, J. A., Jul 5 2012, In : PLoS One. 7, 7, e40389.

Research output: Contribution to journalArticle

oncogenes
Oncogenes
Chromatin
chromatin
testes

Experimental analysis of the mechanism of chromatin remodeling by rna polymerase ii

Gaykalova, D., Kulaeva, O. I., Pestov, N. A., Hsieh, F. K. & Studitsky, V. M., 2012, In : Methods in Enzymology. 512, p. 293-314 22 p.

Research output: Contribution to journalArticle

Chromatin Assembly and Disassembly
DNA-Directed RNA Polymerases
Chromatin
Genes
RNA Polymerase II

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

Shao, C., Tan, M., Bishop, J. A., Liu, J., Bai, W., Gaykalova, D., Ogawa, T., Vikani, A. R., Agrawal, Y., Li, R. J., Kim, M. S., Westra, W. H., Sidransky, D., Califano, J. A. & Ha, P. K., Nov 7 2012, In : PLoS One. 7, 11, e48582.

Research output: Contribution to journalArticle

decitabine
trichostatin A
Adenoid Cystic Carcinoma
CpG Islands
Methylation
2011

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

Gaykalova, D., Nagarajavel, V., Bondarenko, V. A., Bartholomew, B., Clark, D. J. & Studitsky, V. M., May 2011, In : Nucleic Acids Research. 39, 9, p. 3520-3528 9 p.

Research output: Contribution to journalArticle

Nucleosomes
Histones
Chromatin
RNA Polymerase II
Genes

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

Bhan, S., Negi, S. S., Shao, C., Glazer, C. A., Chuang, A., Gaykalova, D., Sun, W., Sidransky, D., Ha, P. K. & Califano, J. A., Jul 1 2011, In : Clinical Cancer Research. 17, 13, p. 4267-4276 10 p.

Research output: Contribution to journalArticle

Histone Code
Testicular Neoplasms
Methylation
Transcriptional Activation
Lung Neoplasms
2009

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

Kulaeva, O. I., Gaykalova, D., Pestov, N. A., Golovastov, V. V., Vassylyev, D. G., Artsimovitch, I. & Studitsky, V. M., Dec 2009, In : Nature Structural and Molecular Biology. 16, 12, p. 1272-1278 7 p.

Research output: Contribution to journalArticle

Chromatin Assembly and Disassembly
Nucleosomes
RNA Polymerase II
Histones
DNA

Preparation and analysis of uniquely positioned mononucleosomes.

Gaykalova, D., Kulaeva, O. I., Bondarenko, V. A. & Studitsky, V. M., 2009, In : Methods in molecular biology (Clifton, N.J.). 523, p. 109-123 15 p.

Research output: Contribution to journalArticle

Nucleosomes
Chromatin Assembly and Disassembly
DNA
Systems Analysis
DNA Repair

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

Morozov, A. V., Fortney, K., Gaykalova, D., Studitsky, V. M., Widom, J. & Siggia, E. D., 2009, In : Nucleic Acids Research. 37, 14, p. 4707-4722 16 p.

Research output: Contribution to journalArticle

Nucleosomes
Mechanics
DNA
Histones
Chromatin Assembly and Disassembly
2007

Transcription through chromatin by RNA polymerase II: Histone displacement and exchange

Kulaeva, O. I., Gaykalova, D. & Studitsky, V. M., May 1 2007, In : Mutation Research - Fundamental and Molecular Mechanisms of Mutagenesis. 618, 1-2, p. 116-129 14 p.

Research output: Contribution to journalArticle

RNA Polymerase II
Histones
Chromatin
DNA
Proteins
2006

Nucleosomes Can Form a Polar Barrier to Transcript Elongation by RNA Polymerase II

Bondarenko, V. A., Steele, L. M., Újvári, A., Gaykalova, D., Kulaeva, O. I., Polikanov, Y. S., Luse, D. S. & Studitsky, V. M., Nov 3 2006, In : Molecular Cell. 24, 3, p. 469-479 11 p.

Research output: Contribution to journalArticle

Nucleosomes
RNA Polymerase II
DNA
Salts
Histones