Examining the contribution of smoking and HPV towards the etiology of oral cavity squamous cell carcinoma using high-throughput sequencing: A prospective observational study

GenVisR: Genomic Visualizations in R

(2016) Zachary L. Skidmore et al.   BIOINFORMATICS

Analyzing and interpreting genome data at the network level with ConsensusPathDB

(2016) Ralf Herwig et al.   Nature Protocols

Missense mutations in the TP53 DNA-binding domain predict outcomes in patients with advanced oral cavity squamous cell carcinoma

(2016) Nina Lapke et al.   Oncotarget

Global cancer statistics, 2012

(2015) Lindsey A. Torre et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Oncotator: Cancer Variant Annotation Tool

(2015) Alex H. Ramos et al.   HUMAN MUTATION

Nicotine Induces Tumor Growth and Chemoresistance through Activation of the PI3K/Akt/mTOR Pathway in Bladder Cancer

(2015) K. Yuge et al.   MOLECULAR CANCER THERAPEUTICS

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

BubbleTree: an intuitive visualization to elucidate tumoral aneuploidy and clonality using next generation sequencing data

(2015) Wei Zhu et al.   NUCLEIC ACIDS RESEARCH

mTOR and MEK1/2 inhibition differentially modulate tumor growth and the immune microenvironment in syngeneic models of oral cavity cancer

(2015) Harrison Cash et al.   Oncotarget

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

The prevalence of human papilloma virus (HPV) infections in oral squamous cell carcinomas: A retrospective analysis of 88 patients and literature overview

(2014) M. Krüger et al.   JOURNAL OF CRANIO-MAXILLOFACIAL SURGERY

Therapeutic Priority of the PI3K/AKT/mTOR Pathway in Small Cell Lung Cancers as Revealed by a Comprehensive Genomic Analysis

(2014) Shigeki Umemura et al.   Journal of Thoracic Oncology

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law et al.   GENOME BIOLOGY

p16 Immunohistochemistry Can Be Used to Detect Human Papillomavirus in Oral Cavity Squamous Cell Carcinoma

(2013) Lisa D. Duncan et al.   JOURNAL OF ORAL AND MAXILLOFACIAL SURGERY

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

Oral Cavity and Oropharyngeal Squamous Cell Carcinoma Genomics

(2013) Marietta Tan et al.   OTOLARYNGOLOGIC CLINICS OF NORTH AMERICA

Cyclin D1, EGFR, and Akt/mTOR pathway

(2013) D. Dionysopoulos et al.   STRAHLENTHERAPIE UND ONKOLOGIE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

Partial p16 staining in oropharyngeal squamous cell carcinoma: extent and pattern correlate with human papillomavirus RNA status

(2012) James S Lewis et al.   MODERN PATHOLOGY

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Cigarette Smoke Components Induce Matrix Metalloproteinase-1 in Aortic Endothelial Cells through Inhibition of mTOR Signaling

(2011) Vincent Lemaître et al.   TOXICOLOGICAL SCIENCES

Human papillomavirus (HPV)-positive tonsillar carcinomas are frequent and have a favourable prognosis in males in Norway

(2010) Kirsten Hannisdal et al.   ACTA OTO-LARYNGOLOGICA

Expression of p16 in oral cancer and premalignant lesions

(2010) Waranun Buajeeb et al.   JOURNAL OF ORAL PATHOLOGY & MEDICINE

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Interaction between Tobacco and Alcohol Use and the Risk of Head and Neck Cancer: Pooled Analysis in the International Head and Neck Cancer Epidemiology Consortium

(2009) M. Hashibe et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

The Role of the Akt/mTOR Pathway in Tobacco Carcinogen-Induced Lung Tumorigenesis

(2009) R. M. Memmott et al.   CLINICAL CANCER RESEARCH

Biological and clinical relevance of transcriptionally active human papillomavirus (HPV) infection in oropharynx squamous cell carcinoma

(2009) Alain C. Jung et al.   INTERNATIONAL JOURNAL OF CANCER

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Recent Advances in Head and Neck Cancer

(2008) Robert I. Haddad et al.   NEW ENGLAND JOURNAL OF MEDICINE