Chromatin dysregulation associated with NSD1 mutation in head and neck squamous cell carcinoma

Twist-1 is upregulated by NSD2 and contributes to tumour dissemination and an epithelial-mesenchymal transition-like gene expression signature in t(4;14)-positive multiple myeloma

(2020) Chee Man Cheong et al.   CANCER LETTERS

Global Regulation of the Histone Mark H3K36me2 Underlies Epithelial Plasticity and Metastatic Progression

(2020) Salina Yuan et al.   Cancer Discovery

HPV, tumour metabolism and novel target identification in head and neck squamous cell carcinoma

(2019) Jason C. Fleming et al.   BRITISH JOURNAL OF CANCER

Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers

(2019) Zhe Ji et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

EZH2 oncogenic mutations drive epigenetic, transcriptional, and structural changes within chromatin domains

(2019) Maria C. Donaldson-Collier et al.   NATURE GENETICS

refTSS: A Reference Data Set for Human and Mouse Transcription Start Sites

(2019) Imad Abugessaisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Targeting DNA Methylation and EZH2 Activity to Overcome Melanoma Resistance to Immunotherapy

(2019) Abdullah Al Emran et al.   TRENDS IN IMMUNOLOGY

The ENCODE Blacklist: Identification of Problematic Regions of the Genome

(2019) Haley M. Amemiya et al.   Scientific Reports

The histone mark H3K36me2 recruits DNMT3A and shapes the intergenic DNA methylation landscape

(2019) Daniel N. Weinberg et al.   NATURE

Immune profiles in primary squamous cell carcinoma of the head and neck

(2019) Vassiliki Saloura et al.   ORAL ONCOLOGY

The Impact of One Carbon Metabolism on Histone Methylation

(2019) Magdalini Serefidou et al.   Frontiers in Genetics

NSD2 overexpression drives clustered chromatin and transcriptional changes in a subset of insulated domains

(2019) Priscillia Lhoumaud et al.   Nature Communications

De novo truncating variants in WHSC1 recapitulate the Wolf–Hirschhorn (4p16.3 microdeletion) syndrome phenotype

(2018) Nada Derar et al.   GENETICS IN MEDICINE

EpiProfile 2.0: A Computational Platform for Processing Epi-Proteomics Mass Spectrometry Data

(2018) Zuo-Fei Yuan et al.   JOURNAL OF PROTEOME RESEARCH

Disruption ofNSD1in Head and Neck Cancer Promotes Favorable Chemotherapeutic Responses Linked to Hypomethylation

(2018) Nam Bui et al.   MOLECULAR CANCER THERAPEUTICS

The H3K36me2 Methyltransferase Nsd1 Demarcates PRC2-Mediated H3K27me2 and H3K27me3 Domains in Embryonic Stem Cells

(2018) Gundula Streubel et al.   MOLECULAR CELL

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

Improved identification of concordant and discordant gene expression signatures using an updated rank-rank hypergeometric overlap approach

(2018) Kelly M. Cahill et al.   Scientific Reports

Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids

(2018) Anthony M. D'Ippolito et al.   Cell Systems

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The chromatin accessibility landscape of primary human cancers

(2018) M. Ryan Corces et al.   SCIENCE

Impaired H3K36 methylation defines a subset of head and neck squamous cell carcinomas

(2017) Simon Papillon-Cavanagh et al.   NATURE GENETICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Poor oral health affects survival in head and neck cancer

(2017) Douglas R. Farquhar et al.   ORAL ONCOLOGY

NSD1- and NSD2-damaging mutations define a subset of laryngeal tumors with favorable prognosis

(2017) Suraj Peri et al.   Nature Communications

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

(2017) Simon Fishilevich et al.   Database-The Journal of Biological Databases and Curation

Ten Years of Progress in Head and Neck Cancers

(2017) Shrujal Baxi et al.   Journal of the National Comprehensive Cancer Network

NSD1 inactivation defines an immune cold, DNA hypomethylated subtype in squamous cell carcinoma

(2017) Kevin Brennan et al.   Scientific Reports

The role of oral hygiene in head and neck cancer: results from International Head and Neck Cancer Epidemiology (INHANCE) consortium

(2016) D. Hashim et al.   ANNALS OF ONCOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape

(2016) C. Lu et al.   SCIENCE

NSD2 contributes to oncogenic RAS-driven transcription in lung cancer cells through long-range epigenetic activation

(2016) Verónica García-Carpizo et al.   Scientific Reports

LOLA: enrichment analysis for genomic region sets and regulatory elements in R and Bioconductor

(2015) Nathan C. Sheffield et al.   BIOINFORMATICS

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Human Papillomavirus–Negative Pharyngeal Cancer

(2015) Magnus T. Dillon et al.   JOURNAL OF CLINICAL ONCOLOGY

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(2015) David G. Pfister et al.   Journal of the National Comprehensive Cancer Network

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

NSD1 mutations generate a genome-wide DNA methylation signature

(2015) S. Choufani et al.   Nature Communications

Correction: Intra-tumor Genetic Heterogeneity and Mortality in Head and Neck Cancer: Analysis of Data from The Cancer Genome Atlas

(2015)   PLOS MEDICINE

Pancancer analysis of DNA methylation-driven genes using MethylMix

(2015) Olivier Gevaert et al.   GENOME BIOLOGY

The Ensembl Regulatory Build

(2015) Daniel R Zerbino et al.   GENOME BIOLOGY

Interplay between Transcription Factors and the Epigenome: Insight from the Role of RUNX1 in Leukemia

(2015) Kate H. Brettingham-Moore et al.   Frontiers in Immunology

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

An updated overview of HPV-associated head and neck carcinomas

(2015) Apostolos Zaravinos   Oncotarget

Integrative and Comparative Genomic Analysis of HPV-Positive and HPV-Negative Head and Neck Squamous Cell Carcinomas

(2014) Tanguy Y. Seiwert et al.   CLINICAL CANCER RESEARCH

The NSD 1 and EZH 2 Overgrowth Genes, Similarities and Differences

(2013) KATRINA TATTON-BROWN et al.   AMERICAN JOURNAL OF MEDICAL GENETICS PART C-SEMINARS IN MEDICAL GENETICS

Finding the active genes in deep RNA-seq gene expression studies

(2013) Traver Hart et al.   BMC GENOMICS

Point mutation E1099K in MMSET/NSD2 enhances its methyltranferase activity and leads to altered global chromatin methylation in lymphoid malignancies

(2013) J A Oyer et al.   LEUKEMIA

Global chromatin profiling reveals NSD2 mutations in pediatric acute lymphoblastic leukemia

(2013) Jacob D Jaffe et al.   NATURE GENETICS

Investigating the association between oral hygiene and head and neck cancer

(2013) Jeffrey S. Chang et al.   ORAL ONCOLOGY

Oral cavity and oropharyngeal squamous cell carcinoma in young adults: a review of the literature

(2013) Ewa Majchrzak et al.   Radiology and Oncology

SET for life: biochemical activities and biological functions of SET domain-containing proteins

(2013) Hans-Martin Herz et al.   TRENDS IN BIOCHEMICAL SCIENCES

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Robust rank aggregation for gene list integration and meta-analysis

(2012) Raivo Kolde et al.   BIOINFORMATICS

Differential oestrogen receptor binding is associated with clinical outcome in breast cancer

(2012) Caryn S. Ross-Innes et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Topological domains in mammalian genomes identified by analysis of chromatin interactions

(2012) Jesse R. Dixon et al.   NATURE

The histone methyltransferase MMSET/WHSC1 activates TWIST1 to promote an epithelial–mesenchymal transition and invasive properties of prostate cancer

(2012) T Ezponda et al.   ONCOGENE

Sotos Syndrome Is Associated with Deregulation of the MAPK/ERK-Signaling Pathway

(2012) Remco Visser et al.   PLoS One

The Structure of NSD1 Reveals an Autoregulatory Mechanism Underlying Histone H3K36 Methylation

(2011) Qi Qiao et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Oral Health Literacy among Female Caregivers

(2010) W.F. Vann et al.   JOURNAL OF DENTAL RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Human Papillomavirus and Survival of Patients with Oropharyngeal Cancer

(2010) K. Kian Ang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Human Papillomavirus in Head and Neck Cancer: Its Role in Pathogenesis and Clinical Implications

(2009) C. H. Chung et al.   CLINICAL CANCER RESEARCH

Improved Survival of Patients With Human Papillomavirus-Positive Head and Neck Squamous Cell Carcinoma in a Prospective Clinical Trial

(2008) C. Fakhry et al.   JNCI-Journal of the National Cancer Institute

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY