Pan-cancer multi-omics analysis and orthogonal experimental assessment of epigenetic driver genes

Passenger Hotspot Mutations in Cancer

(2019) Julian M. Hess et al.   CANCER CELL

Revisiting the tumorigenesis timeline with a data-driven generative model

(2019) Kamel Lahouel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Systematic Functional Annotation of Somatic Mutations in Cancer

(2018) Patrick Kwok-Shing Ng et al.   CANCER CELL

Perspective on Oncogenic Processes at the End of the Beginning of Cancer Genomics

(2018) Li Ding et al.   CELL

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Epigenetic Therapeutics: A New Weapon in the War Against Cancer

(2016) Nita Ahuja et al.   Annual Review of Medicine

Exploiting the Epigenome to Control Cancer-Promoting Gene-Expression Programs

(2016) Gerard L. Brien et al.   CANCER CELL

Targeting the cancer epigenome for therapy

(2016) Peter A. Jones et al.   NATURE REVIEWS GENETICS

OUP accepted manuscript

(2016)   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens

(2015) Jan Winter et al.   BIOINFORMATICS

An integrative pan-cancer-wide analysis of epigenetic enzymes reveals universal patterns of epigenomic deregulation in cancer

(2015) Zhen Yang et al.   GENOME BIOLOGY

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Interplay between the Cancer Genome and Epigenome

(2013) Hui Shen et al.   CELL

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

The epigenetics of epithelial-mesenchymal plasticity in cancer

(2013) Wai Leong Tam et al.   NATURE MEDICINE

Mutations in regulators of the epigenome and their connections to global chromatin patterns in cancer

(2013) Christoph Plass et al.   NATURE REVIEWS GENETICS

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

The mutational landscape of chromatin regulatory factors across 4,623 tumor samples

(2013) Abel Gonzalez-Perez et al.   GENOME BIOLOGY

TSGene: a web resource for tumor suppressor genes

(2012) Min Zhao et al.   NUCLEIC ACIDS RESEARCH

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Determinants and dynamics of genome accessibility

(2011) Oliver Bell et al.   NATURE REVIEWS GENETICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function

(2010) David Warde-Farley et al.   NUCLEIC ACIDS RESEARCH

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Design and analysis issues in genome-wide somatic mutation studies of cancer

(2008) Giovanni Parmigiani et al.   GENOMICS

Epigenetic drivers and genetic passengers on the road to cancer

(2008) Carla Sawan et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS