Decoding the regulatory landscape of melanoma reveals TEADS as regulators of the invasive cell state

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

(2014) S. Anders et al.   BIOINFORMATICS

Genome-wide Profiling of AP-1-Regulated Transcription Provides Insights into the Invasiveness of Triple-Negative Breast Cancer

(2014) C. Zhao et al.   CANCER RESEARCH

Hippo Coactivator YAP1 Upregulates SOX9 and Endows Esophageal Cancer Cells with Stem-like Properties

(2014) S. Song et al.   CANCER RESEARCH

YAP/TAZ Incorporation in the β-Catenin Destruction Complex Orchestrates the Wnt Response

(2014) Luca Azzolin et al.   CELL

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma

(2014) Chong Sun et al.   NATURE

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Global view of enhancer-promoter interactome in human cells

(2014) B. He et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Low MITF/AXL ratio predicts early resistance to multiple targeted drugs in melanoma

(2014) Judith Müller et al.   Nature Communications

A Melanoma Cell State Distinction Influences Sensitivity to MAPK Pathway Inhibitors

(2014) D. J. Konieczkowski et al.   Cancer Discovery

iRegulon: From a Gene List to a Gene Regulatory Network Using Large Motif and Track Collections

(2014) Rekin's Janky et al.   PLoS Computational Biology

Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser

(2013) B. J. Raney et al.   BIOINFORMATICS

Directed Phenotype Switching as an Effective Antimelanoma Strategy

(2013) Magalí Sáez-Ayala et al.   CANCER CELL

A Switch in the Expression of Embryonic EMT-Inducers Drives the Development of Malignant Melanoma

(2013) Julie Caramel et al.   CANCER CELL

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

(2013) Jian Yan et al.   CELL

Pro-Invasive Activity of the Hippo Pathway Effectors YAP and TAZ in Cutaneous Melanoma

(2013) Flore Nallet-Staub et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data

(2013) Supat Thongjuea et al.   NUCLEIC ACIDS RESEARCH

Epigenetic Reprogramming in Cancer

(2013) M. L. Suva et al.   SCIENCE

Viral Capsid Proteins Are Segregated in Structural Fold Space

(2013) Shanshan Cheng et al.   PLoS Computational Biology

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Determining long-range chromatin interactions for selected genomic sites using 4C-seq technology: From fixation to computation

(2012) Erik Splinter et al.   METHODS

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Sox10 promotes the formation and maintenance of giant congenital naevi and melanoma

(2012) Olga Shakhova et al.   NATURE CELL BIOLOGY

MDM4 is a key therapeutic target in cutaneous melanoma

(2012) Agnieszka Gembarska et al.   NATURE MEDICINE

i-cisTarget: an integrative genomics method for the prediction of regulatory features and cis-regulatory modules

(2012) Carl Herrmann et al.   NUCLEIC ACIDS RESEARCH

Systematic classification of melanoma cells by phenotype-specific gene expression mapping

(2012) Daniel S. Widmer et al.   Pigment Cell & Melanoma Research

12-Chemokine Gene Signature Identifies Lymph Node-like Structures in Melanoma: Potential for Patient Selection for Immunotherapy?

(2012) Jane L. Messina et al.   Scientific Reports

inSilicoDb: an R/Bioconductor package for accessing human Affymetrix expert-curated datasets from GEO

(2011) J. Taminau et al.   BIOINFORMATICS

The Hippo Transducer TAZ Confers Cancer Stem Cell-Related Traits on Breast Cancer Cells

(2011) Michelangelo Cordenonsi et al.   CELL

The transcriptional coactivator TAZ regulates mesenchymal differentiation in malignant glioma

(2011) K. P. L. Bhat et al.   GENES & DEVELOPMENT

Transcriptional Activation of ZEB1 by Slug Leads to Cooperative Regulation of the Epithelial–Mesenchymal Transition-Like Phenotype in Melanoma

(2011) Christian Wels et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Human Cutaneous Melanomas Lacking MITF and Melanocyte Differentiation Antigens Express a Functional Axl Receptor Kinase

(2011) Marialuisa Sensi et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

Transcription factor Sox10 orchestrates activity of a neural crest-specific enhancer in the vicinity of its gene

(2011) M. Wahlbuhl et al.   NUCLEIC ACIDS RESEARCH

Epha2 is a critical oncogene in melanoma

(2011) D Udayakumar et al.   ONCOGENE

Essential role of microphthalmia transcription factor for DNA replication, mitosis and genomic stability in melanoma

(2011) T Strub et al.   ONCOGENE

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

Hippo signaling: growth control and beyond

(2010) G. Halder et al.   DEVELOPMENT

Integrating multiple evidence sources to predict transcription factor binding in the human genome

(2010) J. Ernst et al.   GENOME RESEARCH

Cancer stem cells versus phenotype-switching in melanoma

(2010) Keith S. Hoek et al.   Pigment Cell & Melanoma Research

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

TEAD Transcription Factors Mediate the Function of TAZ in Cell Growth and Epithelial-Mesenchymal Transition

(2009) Heng Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde Assisted Isolation of Regulatory Elements)

(2009) Paul G. Giresi et al.   METHODS

F-Seq: a feature density estimator for high-throughput sequence tags

(2008) A. P. Boyle et al.   BIOINFORMATICS

In vivo Switching of Human Melanoma Cells between Proliferative and Invasive States

(2008) K. S. Hoek et al.   CANCER RESEARCH

SOX9 Is Expressed in Human Fetal Prostate Epithelium and Enhances Prostate Cancer Invasion

(2008) H. Wang et al.   CANCER RESEARCH

Novel MITF targets identified using a two-step DNA microarray strategy

(2008) Keith S. Hoek et al.   Pigment Cell & Melanoma Research

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY