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Author Details

Daria A Gaykalova
Institute for Genome Sciences, University of Maryland School of Medicine
2006
57
25
Trey Ideker (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37674725Identification of CT-based non-invasive Radiographic Biomarkers for Overall Survival Stratification in Oral Cavity Squamous Cell Carcinoma.Res Sq2023
37662332Insights into the Mechanisms and Structure of Breakage-Fusion-Bridge Cycles in Cervical Cancer using Long-Read Sequencing.medRxiv2023
35201318Entinostat Decreases Immune Suppression to Promote Antitumor Responses in a HER2+ Breast Tumor Microenvironment.Cancer Immunol Res2022
35667295Simultaneously targeting ErbB family kinases and PI3K in HPV-positive head and neck squamous cell carcinoma.Oral Oncol2022
35571032Epigenetic Regulations of Perineural Invasion in Head and Neck Squamous Cell Carcinoma.Front Genet2022
35016036The use of machine learning to discover regulatory networks controlling biological systems.Mol Cell2022
34589558Correction: Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor.Oncoscience2021
32164487Chromatin structure regulates cancer-specific alternative splicing events in primary HPV-related oropharyngeal squamous cell carcinoma.Epigenetics2020
31830557Somatic mitochondrial mutation discovery using ultra-deep sequencing of the mitochondrial genome reveals spatial tumor heterogeneity in head and neck squamous cell carcinoma.Cancer Lett2020
33015029Extracellular Vesicles Released by Tumor Endothelial Cells Spread Immunosuppressive and Transforming Signals Through Various Recipient Cells.Front Cell Dev Biol2020
32848210HPV E2, E4, E5 drive alternative carcinogenic pathways in HPV positive cancers.Oncogene2020
32694696Correction: 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.Br J Cancer2020
32392348Matrix factorization and transfer learning uncover regulatory biology across multiple single-cell ATAC-seq data sets.Nucleic Acids Res2020
32362655Integrated 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.Br J Cancer2020
32401780Correction: Novel Insight into Mutational Landscape of Head and Neck Squamous Cell Carcinoma.PLoS One2020
31002670CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer.PLoS Comput Biol2019
31636280Differentially Methylated Super-Enhancers Regulate Target Gene Expression in Human Cancer.Sci Rep2019
31097695Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.Nat Commun2019
31142745Publisher Correction: Chromatin dysregulation and DNA methylation at transcription start sites associated with transcriptional repression in cancers.Nat Commun2019
29342249Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.Bioinformatics2018
29909892HEY1 is expressed independent of NOTCH1 and is associated with poor prognosis in head and neck squamous cell carcinoma.Oral Oncol2018
30070359Discovery and development of differentially methylated regions in human papillomavirus-related oropharyngeal squamous cell carcinoma.Int J Cancer2018
30118659Functional characterization of alternatively spliced GSN in head and neck squamous cell carcinoma.Transl Res2018
30514962PDGF enhances the protective effect of adipose stem cell-derived extracellular vesicles in a model of acute hindlimb ischemia.Sci Rep2018
30341436Structural interpretation of DNA-protein hydroxyl-radical footprinting experiments with high resolution using HYDROID.Nat Protoc2018
29792227Integrated time course omics analysis distinguishes immediate therapeutic response from acquired resistance.Genome Med2018
29556515Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor.Oncoscience2018
28968850Epigenetic regulation of gene expression in cancer: techniques, resources and analysis.Brief Funct Genomics2018
28733453A Novel Functional Splice Variant of <i>AKT3</i> Defined by Analysis of Alternative Splice Expression in HPV-Positive Oropharyngeal Cancers.Cancer Res2017
28146432Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC.Oncotarget2017
28174896PatternMarkers &amp; GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.Bioinformatics2017
29123240DNA methylation regulates TMEM16A/ANO1 expression through multiple CpG islands in head and neck squamous cell carcinoma.Sci Rep2017
28947419Integrated 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.Cancer Res2017
28619685Molecular mechanisms of human papillomavirus-related carcinogenesis in head and neck cancer.Microbes Infect2017
28580171<i>In silico</i> analysis of pathways activation landscape in oral squamous cell carcinoma and oral leukoplakia.Cell Death Discov2017
26949921Characterization of functionally active gene fusions in human papillomavirus related oropharyngeal squamous cell carcinoma.Int J Cancer2016
27650546CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network.Oncotarget2016
26884679Toward Signaling-Driven Biomarkers Immune to Normal Tissue Contamination.Cancer Inform2016
26701665Serum Antibodies to HPV16 Early Proteins Warrant Investigation as Potential Biomarkers for Risk Stratification and Recurrence of HPV-Associated Oropharyngeal Cancer.Cancer Prev Res (Phila)2016
25857630NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma.Int J Cancer2015
26544568Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients.PLoS One2015
26460019Structural analysis of nucleosomal barrier to transcription.Proc Natl Acad Sci U S A2015
24351288Activation of the NOTCH pathway in head and neck cancer.Cancer Res2014
25195578Correcting transcription factor gene sets for copy number and promoter methylation variations.Drug Dev Res2014
24667986Novel insight into mutational landscape of head and neck squamous cell carcinoma.PLoS One2014
24675808Expression microarray analysis reveals alternative splicing of LAMA3 and DST genes in head and neck squamous cell carcinoma.PLoS One2014
24223768Preferential activation of the hedgehog pathway by epigenetic modulations in HPV negative HNSCC identified with meta-pathway analysis.PLoS One2013
22910212Experimental analysis of the mechanism of chromatin remodeling by RNA polymerase II.Methods Enzymol2012
23144906Suprabasin is hypomethylated and associated with metastasis in salivary adenoid cystic carcinoma.PLoS One2012
22792300Dose-dependent activation of putative oncogene SBSN by BORIS.PLoS One2012
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Collaborators

Elana J Fertig
Johns Hopkins University School of Medicine
Co-authored papers 29
Joseph A Califano
University of California
Co-authored papers 27
Alexander V Favorov
Johns Hopkins School of Medicine
Co-authored papers 17
Theresa Guo
Moores Cancer Center, University of California
Co-authored papers 16
Michael J Considine
Johns Hopkins University School of Medicine
Co-authored papers 14
Justin A Bishop
UT Southwestern Medical Center
Co-authored papers 14
Ludmila Danilova
Bloomberg-Kimmel Immunotherapy Institute, Johns Hopkins University School of Medicine
Co-authored papers 14
Michael F Ochs
The College of New Jersey
Co-authored papers 13
Wayne M Koch
Johns Hopkins University School of Medicine
Co-authored papers 12
William H Westra
Icahn School of Medicine at Mount Sinai Hospital.
Co-authored papers 11
Ryan Li
Oregon Health & Science University
Co-authored papers 7
Zubair Khan
University of Texas at Houston Health Science Center
Co-authored papers 7
Patrick K Ha
University of California San Francisco
Co-authored papers 7
Sarah J Wheelan
National Human Genome Research Institute, National Institutes of Health
Co-authored papers 6
Srinivasan Yegnasubramanian
Johns Hopkins University School of Medicine
Co-authored papers 6
Genevieve L Stein-O'Brien
Johns Hopkins School of Medicine
Co-authored papers 6
Akihiro Sakai
Tokai University
Co-authored papers 5
Shuling Ren
Beijing Friendship Hospital, Capital Medical University
Co-authored papers 4
Trey Ideker (CM4AI)
University of California San Diego
Co-authored papers 4
Mizuo Ando
University of Tokyo
Co-authored papers 4
Takahito Fukusumi
Osaka University Graduate School of Medicine
Co-authored papers 4
Chao Liu
Xiangya Hospital, Central South University
Co-authored papers 4
Kathleen M Fisch
Center for Computational Biology and Bioinformatics, University of California
Co-authored papers 3
Jorge Silvio Gutkind
Moores Cancer Center, University of California San Diego
Co-authored papers 3
Guorong Xu
Chinese University of Hong Kong
Co-authored papers 3
Pablo Tamayo
University of California San Diego
Co-authored papers 3
Sunny Haft
Moores Cancer Center, University of California
Co-authored papers 3
Yuki Saito
Niigata Prefectural Tokamachi Hospital.
Co-authored papers 2
Kate Medetgul-Ernar
University of California San Diego Health Moores Cancer Center.
Co-authored papers 2
John Pang
University of Washington
Co-authored papers 2
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