Integrated genomic and molecular characterization of cervical cancer

Molecular and Genetic Properties of Tumors Associated with Local Immune Cytolytic Activity

(2015) Michael S. Rooney et al.   CELL

Genomic aberrations in cervical adenocarcinomas in Hong Kong Chinese women

(2015) Tony K.H. Chung et al.   INTERNATIONAL JOURNAL OF CANCER

Comprehensive genomic characterization of head and neck squamous cell carcinomas

(2015)   NATURE

Molecular transitions from papillomavirus infection to cervical precancer and cancer: Role of stromal estrogen receptor signaling

(2015) Johan A. den Boon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control

(2014) Yinming Jiao et al.   BIOINFORMATICS

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

(2014) Justin Chu et al.   BIOINFORMATICS

KRAS and YAP1 Converge to Regulate EMT and Tumor Survival

(2014) Diane D. Shao et al.   CELL

Integrated Genomic Characterization of Papillary Thyroid Carcinoma

(2014) Nishant Agrawal et al.   CELL

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

(2014) Katherine A. Hoadley et al.   CELL

Cancer incidence and mortality worldwide: Sources, methods and major patterns in GLOBOCAN 2012

(2014) Jacques Ferlay et al.   INTERNATIONAL JOURNAL OF CANCER

Microenvironment-dependent cues trigger miRNA-regulated feedback loop to facilitate the EMT/MET switch

(2014) Julienne L. Carstens et al.   JOURNAL OF CLINICAL INVESTIGATION

Comprehensive molecular characterization of urothelial bladder carcinoma

(2014)   NATURE

Transforming RNA-Seq Data to Improve the Performance of Prognostic Gene Signatures

(2014) Isabella Zwiener et al.   PLoS One

A pan-cancer proteomic perspective on The Cancer Genome Atlas

(2014) Rehan Akbani et al.   Nature Communications

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

(2014) Stephen Henderson et al.   Cell Reports

Learning subgroup-specific regulatory interactions and regulator independence with PARADIGM

(2013) Andrew J. Sedgewick et al.   BIOINFORMATICS

Oncogenic ERBB3 Mutations in Human Cancers

(2013) Bijay S. Jaiswal et al.   CANCER CELL

Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes

(2013) Lixing Yang et al.   CELL

Genomics of Cervical Cancer and the Role of Human Papillomavirus Pathobiology

(2013) D. Uyar et al.   CLINICAL CHEMISTRY

A core microRNA signature associated with inducers of the epithelial-to-mesenchymal transition

(2013) Juan Díaz-Martín et al.   JOURNAL OF PATHOLOGY

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Landscape of genomic alterations in cervical carcinomas

(2013) Akinyemi I. Ojesina et al.   NATURE

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

(2013) Michael S. Lawrence et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Evidence for APOBEC3B mutagenesis in multiple human cancers

(2013) Michael B Burns et al.   NATURE GENETICS

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

The epigenetics of epithelial-mesenchymal plasticity in cancer

(2013) Wai Leong Tam et al.   NATURE MEDICINE

miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions

(2013) Sheng-Da Hsu et al.   NUCLEIC ACIDS RESEARCH

MicroRNAs regulate both epithelial-to-mesenchymal transition and cancer stem cells

(2013) P Ceppi et al.   ONCOGENE

The papillomavirus E7 proteins

(2013) Ann Roman et al.   VIROLOGY

Papillomavirus E6 oncoproteins

(2013) Scott B. Vande Pol et al.   VIROLOGY

EMT transcription factors snail and slug directly contribute to cisplatin resistance in ovarian cancer

(2012) Alexandria M Haslehurst et al.   BMC CANCER

BCAR4 induces antioestrogen resistance but sensitises breast cancer to lapatinib

(2012) M F E Godinho et al.   BRITISH JOURNAL OF CANCER

An Epithelial-Mesenchymal Transition Gene Signature Predicts Resistance to EGFR and PI3K Inhibitors and Identifies Axl as a Therapeutic Target for Overcoming EGFR Inhibitor Resistance

(2012) L. A. Byers et al.   CLINICAL CANCER RESEARCH

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Comprehensive genomic characterization of squamous cell lung cancers

(2012)   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

TGFβ signalling in context

(2012) Joan Massagué   NATURE REVIEWS MOLECULAR CELL BIOLOGY

14-3-3σ Regulates β-Catenin-Mediated Mouse Embryonic Stem Cell Proliferation by Sequestering GSK-3β

(2012) Tzu-Ching Chang et al.   PLoS One

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

UM-SCC-104: A New human papillomavirus-16-positive cancer stem cell-containing head and neck squamous cell carcinoma cell line

(2011) Alice L. Tang et al.   HEAD AND NECK-JOURNAL FOR THE SCIENCES AND SPECIALTIES OF THE HEAD AND NECK

Human Papillomavirus Testing in the Prevention of Cervical Cancer

(2011) Mark Schiffman et al.   JNCI-Journal of the National Cancer Institute

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

PathSeq: software to identify or discover microbes by deep sequencing of human tissue

(2011) Aleksandar D Kostic et al.   NATURE BIOTECHNOLOGY

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

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

A Population-Based Prospective Study of Carcinogenic Human Papillomavirus Variant Lineages, Viral Persistence, and Cervical Neoplasia

(2010) M. Schiffman et al.   CANCER RESEARCH

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes

(2010) J. H. Taube et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

(2009) Ronglai Shen et al.   BIOINFORMATICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The role of the ZEB family of transcription factors in development and disease

(2008) C. Vandewalle et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1

(2008) Philip A. Gregory et al.   NATURE CELL BIOLOGY

Integrated detection and population-genetic analysis of SNPs and copy number variation

(2008) Steven A McCarroll et al.   NATURE GENETICS

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

(2008) Joshua M Korn et al.   NATURE GENETICS