ArticleCancer research2017
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.
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Article in Cancer research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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45citing papers in PubMed
1.6field-weighted citation impact, top 18% of its field
What it found
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
45 citing papers in PubMed, 73 citations in OpenAlex.
- Trial
- HOXC6 overexpression stimulates cell migration and correlates with poor prognosis in head and neck squamous cell carcinoma.Cellular and molecular life sciences : CMLS · 2026Article
- Molecular heterogeneity of HPV-associated cancers and strategies to overcome treatment resistance.Cancer heterogeneity and plasticity · 2026Article
- A Roadmap for the Future of Systems Biology in Cancer Research.Cancer research · 2025Review
- Clinical significance of HPV DNA and EGFR mutations in Egyptian NSCLC.Infectious agents and cancer · 2025Article
- Epigenetic profiling reveals key super-enhancer networks driving oncogenesis in HPV-positive HNSCC.iScience · 2025Article
- Human Papillomavirus Integration Induces Oncogenic Host Gene Fusions in Oropharyngeal Cancers.Cancer discovery · 2025Article
- Human papillomavirus genomes associate with active host chromatin during persistent viral infection.PLoS pathogens · 2025Article
- Human Papillomavirus Genomes Associate with Active Host Chromatin during Persistent Viral Infection.bioRxiv : the preprint server for biology · 2025Article
- Comprehensive multimodal and multiomic profiling reveals epigenetic and transcriptional reprogramming in lung tumors.Communications biology · 2025Article
- Inhibition of human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer.Nature communications · 2025Article
- Rewriting cellular fate: epigenetic interventions in obesity and cellular programming.Molecular medicine (Cambridge, Mass.) · 2024Review
- Inhibition of novel human-HPV hybrid ecDNA enhancers reduces oncogene expression and tumor growth in oropharyngeal cancer.Research square · 2024Article
- Article
- Article
- KLF7 regulates super-enhancer-driven IGF2BP2 overexpression to promote the progression of head and neck squamous cell carcinoma.Journal of experimental & clinical cancer research : CR · 2024Article
- PIBF1 regulates multiple gene expression via impeding long-range chromatin interaction to drive the malignant transformation of HPV16 integration epithelial cells.Journal of advanced research · 2024Article
- Human papillomavirus integration transforms chromatin to drive oncogenesis.Genome biology · 2023Article
- VIS Atlas: A Database of Virus Integration Sites in Human Genome from NGS Data to Explore Integration Patterns.Genomics, proteomics & bioinformatics · 2023Article
- A Guide to MethylationToActivity: A Deep Learning Framework That Reveals Promoter Activity Landscapes from DNA Methylomes in Individual Tumors.Methods in molecular biology (Clifton, N.J.) · 2023Article
Corrections and comments
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Authors and funding
22 authors at 3 institutions in 2 countries.
Dylan Z KelleyDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Emily L FlamDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Evgeny IzumchenkoDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Ludmila V DanilovaDepartment of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Hildegard A WulfDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Theresa GuoDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Dzov A SingmanDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Bahman AfsariDepartment of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Alyza M SkaistDepartment of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Michael ConsidineDepartment of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Jane A WelchMcKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Elena StavrovskayaDepartment of Bioengineering and Bioinformatics, Moscow State University, Moscow, Russia.
Justin A BishopDepartment of Pathology, Johns Hopkins Medical School of Medicine, Baltimore, Maryland.
William H WestraDepartment of Pathology, Johns Hopkins Medical School of Medicine, Baltimore, Maryland.
Zubair KhanDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Wayne M KochDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
David SidranskyDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Sarah J WheelanDepartment of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Joseph A CalifanoHead and Neck Cancer Center, Moores Cancer Center, University of California, San Diego, La Jolla, California.
Alexander V FavorovDepartment of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Elana J FertigDepartment of Oncology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
Daria A GaykalovaDepartment of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland. dgaykal1@jhmi.edu.
Johns Hopkins University · USInstitute for Information Transmission Problems · RUNational Foundation for Cancer Research · US
Funding
Translational Research Central ServicesP30CA006973 · NCI · JOHNS HOPKINS UNIVERSITY · PI WILLIAM George NELSON · 1985 to 2026
$208.6MTUMOR SUPPRESOR GENE PROMOTER HYPERMETHYLATION FOR DETECTION OF HEAD AND NECKP50DE019032 · NIDCR · JOHNS HOPKINS UNIVERSITY · PI SIDRANSKY, DAVID · 2007 to 2016
$27.1MEpigenetic Biomarker Discovery in HPV Related HNSCCR01DE023347 · NIDCR · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI CALIFANO, JOSEPH A · 2013 to 2017
$1.9MDynamical Models of Cetuximab Resistance in HNSCC Based on Serial Genomics DataR01CA177669 · NCI · JOHNS HOPKINS UNIVERSITY · PI FERTIG, ELANA · 2014 to 2019
$1.8MCharacterizing genome-wide alternative splicing in HPV related HNSCCR21DE025398 · NIDCR · JOHNS HOPKINS UNIVERSITY · PI GAYKALOVA, DARIA A · 2015 to 2016
$446kNCI NIH HHS P30 CA006973NCI NIH HHS R01 CA177669NIDCR NIH HHS P50 DE019032NIDCR NIH HHS R01 DE023347NIDCR NIH HHS R21 DE025398
Abstract
Chromatin alterations mediate mutations and gene expression changes in cancer. Chromatin immunoprecipitation followed by sequencing (ChIP-Seq) has been utilized to study genome-wide chromatin structure in human cancer cell lines, yet numerous technical challenges limit comparable analyses in primary tumors. Here we have developed a new whole-genome analytic pipeline to optimize ChIP-Seq protocols on patient-derived xenografts from human papillomavirus-related (HPV
Indexed as
Base SequenceCell Line, TumorChromatinChromatin ImmunoprecipitationGene Expression Regulation, NeoplasticGenome, HumanHead and Neck NeoplasmsHumansPapillomaviridaeSequence Analysis, DNAVirus IntegrationChromatin
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.