Analysis of Ugandan cervical carcinomas identifies human papillomavirus clade–specific epigenome and transcriptome landscapes

High expression of PXDN is associated with poor prognosis and promotes proliferation, invasion as well as migration in ovarian cancer

(2018) Ying-Ze Zheng et al.   Annals of Diagnostic Pathology

Peroxidasin is regulated by the epithelial-mesenchymal transition master transcription factor Snai1

(2018) Boitumelo Nonhlanhla Sitole et al.   GENE

KMT2D regulates p63 target enhancers to coordinate epithelial homeostasis

(2018) Enrique Lin-Shiao et al.   GENES & DEVELOPMENT

The curious case of APOBEC3 activation by cancer-associated human papillomaviruses

(2018) Nicholas A. Wallace et al.   PLoS Pathogens

The Dual Role of Neutrophils in HIV Infection

(2018) Tiffany Hensley-McBain et al.   Current HIV/AIDS Reports

Genome-wide discovery of somatic regulatory variants in diffuse large B-cell lymphoma

(2018) Sarah E. Arthur et al.   Nature Communications

Genetic variations in human papillomavirus and cervical cancer outcomes

(2018) Janet S. Rader et al.   INTERNATIONAL JOURNAL OF CANCER

Estimating the global cancer incidence and mortality in 2018: GLOBOCAN sources and methods

(2018) J. Ferlay et al.   INTERNATIONAL JOURNAL OF CANCER

High Prevalence of a Hotspot of Noncoding Somatic Mutations in Intron 6 of GPR126 in Bladder Cancer

(2018) Simon Garinet et al.   MOLECULAR CANCER RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Integrated genomic and molecular characterization of cervical cancer

(2017)   NATURE

Histone Marks in the ‘Driver’s Seat’: Functional Roles in Steering the Transcription Cycle

(2017) Leah A. Gates et al.   TRENDS IN BIOCHEMICAL SCIENCES

The role of integration in oncogenic progression of HPV-associated cancers

(2017) Alison A. McBride et al.   PLoS Pathogens

Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways

(2016) Hye-Jung E. Chun et al.   CANCER CELL

Impact and Effectiveness of the Quadrivalent Human Papillomavirus Vaccine: A Systematic Review of 10 Years of Real-world Experience

(2016) Suzanne M. Garland et al.   CLINICAL INFECTIOUS DISEASES

Effect of HIV Infection on Human Papillomavirus Types Causing Invasive Cervical Cancer in Africa

(2016) Gary M. Clifford et al.   JAIDS-JOURNAL OF ACQUIRED IMMUNE DEFICIENCY SYNDROMES

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

HPV16 oncogene expression levels during early cervical carcinogenesis are determined by the balance of epigenetic chromatin modifications at the integrated virus genome

(2016) I J Groves et al.   ONCOGENE

Analysis of Normal Human Mammary Epigenomes Reveals Cell-Specific Active Enhancer States and Associated Transcription Factor Networks

(2016) Davide Pellacani et al.   Cell Reports

Global estimates of human papillomavirus vaccination coverage by region and income level: a pooled analysis

(2016) Laia Bruni et al.   Lancet Global Health

Need for Radiotherapy in Low and Middle Income Countries – The Silent Crisis Continues

(2015) E.H. Zubizarreta et al.   CLINICAL ONCOLOGY

Activation of the innate immune response by endogenous retroviruses

(2015) Tara P. Hurst et al.   JOURNAL OF GENERAL VIROLOGY

Genome-wide profiling of HPV integration in cervical cancer identifies clustered genomic hot spots and a potential microhomology-mediated integration mechanism

(2015) Zheng Hu et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

Meta-Analysis of DNA Tumor-Viral Integration Site Selection Indicates a Role for Repeats, Gene Expression and Epigenetics

(2015) Janet Doolittle-Hall et al.   Cancers

BioBloom tools: fast, accurate and memory-efficient host species sequence screening using bloom filters

(2014) Justin Chu et al.   BIOINFORMATICS

Multiplatform Analysis of 12 Cancer Types Reveals Molecular Classification within and across Tissues of Origin

(2014) Katherine A. Hoadley et al.   CELL

AnimalTFDB 2.0: a resource for expression, prediction and functional study of animal transcription factors

(2014) Hong-Mei Zhang et al.   NUCLEIC ACIDS RESEARCH

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

APOBEC-Mediated Cytosine Deamination Links PIK3CA Helical Domain Mutations to Human Papillomavirus-Driven Tumor Development

(2014) Stephen Henderson et al.   Cell Reports

ChAMP: 450k Chip Analysis Methylation Pipeline

(2013) Tiffany J. Morris et al.   BIOINFORMATICS

Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells

(2013) Casey A. Gifford et al.   CELL

Unique DNA Methylation Loci Distinguish Anatomic Site and HPV Status in Head and Neck Squamous Cell Carcinoma

(2013) R. A. Lleras et al.   CLINICAL CANCER RESEARCH

CD4+T-cell depletion in HIV infection: mechanisms of immunological failure

(2013) Afam A. Okoye et al.   IMMUNOLOGICAL REVIEWS

The MLL3/MLL4 Branches of the COMPASS Family Function as Major Histone H3K4 Monomethylases at Enhancers

(2013) D. Hu et al.   MOLECULAR AND CELLULAR BIOLOGY

Landscape of genomic alterations in cervical carcinomas

(2013) Akinyemi I. Ojesina et al.   NATURE

TERT Promoter Mutations in Familial and Sporadic Melanoma

(2013) S. Horn et al.   SCIENCE

Highly Recurrent TERT Promoter Mutations in Human Melanoma

(2013) F. W. Huang et al.   SCIENCE

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

H3K4 mono- and di-methyltransferase MLL4 is required for enhancer activation during cell differentiation

(2013) Ji-Eun Lee et al.   eLife

Strelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs

(2012) Christopher T. Saunders et al.   BIOINFORMATICS

Exploring genome-wide DNA methylation profiles altered in hepatocellular carcinoma using Infinium HumanMethylation 450 BeadChips

(2012) Jing Shen et al.   Epigenetics

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Enhancer-associated H3K4 monomethylation by Trithorax-related, the Drosophila homolog of mammalian Mll3/Mll4

(2012) H.-M. Herz et al.   GENES & DEVELOPMENT

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

(2012) S. G. Landt et al.   GENOME RESEARCH

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

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

Feature-based classifiers for somatic mutation detection in tumour–normal paired sequencing data

(2011) Jiarui Ding et al.   BIOINFORMATICS

Validation of a DNA methylation microarray for 450,000 CpG sites in the human genome

(2011) Juan Sandoval et al.   Epigenetics

GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers

(2011) Craig H Mermel et al.   GENOME BIOLOGY

ConsensusClusterPlus: a class discovery tool with confidence assessments and item tracking

(2010) Matthew D. Wilkerson et al.   BIOINFORMATICS

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Human papillomavirus genotype attribution in invasive cervical cancer: a retrospective cross-sectional worldwide study

(2010) Silvia de Sanjose et al.   LANCET ONCOLOGY

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

Persistence of human papillomavirus infection: keys to malignant progression

(2010) Jason Bodily et al.   TRENDS IN MICROBIOLOGY

The critical protein interactions and structures that elicit growth deregulation in cancer and viral replication

(2010) Horng D. Ou et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Classification of weakly carcinogenic human papillomavirus types: addressing the limits of epidemiology at the borderline

(2009) Mark Schiffman et al.   Infectious Agents and Cancer