Identification of High-Impact cis-Regulatory Mutations Using Transcription Factor Specific Random Forest Models

A method to predict the impact of regulatory variants from DNA sequence

(2015) Dongwon Lee et al.   NATURE GENETICS

The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer

(2015) R. J. A. Bell et al.   SCIENCE

Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity

(2014) Matthew T. Weirauch et al.   CELL

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

Systematic analysis of noncoding somatic mutations and gene expression alterations across 14 tumor types

(2014) Nils J Fredriksson et al.   NATURE GENETICS

Transcriptional enhancers: from properties to genome-wide predictions

(2014) Daria Shlyueva et al.   NATURE REVIEWS GENETICS

Identifying causal regulatory SNPs in ChIP-seq enhancers

(2014) Di Huang et al.   NUCLEIC ACIDS RESEARCH

An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element

(2014) M. R. Mansour et al.   SCIENCE

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

The Functional Consequences of Variation in Transcription Factor Binding

(2014) Darren A. Cusanovich et al.   PLoS Genetics

GAT: a simulation framework for testing the association of genomic intervals

(2013) A. Heger et al.   BIOINFORMATICS

TERT promoter mutations in cancer development

(2013) Barbara Heidenreich et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

BLUEPRINT: mapping human blood cell epigenomes

(2013) J. H. A. Martens et al.   HAEMATOLOGICA

Mutations close in on gene regulation

(2013) Stein Aerts et al.   NATURE

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

Emerging landscape of oncogenic signatures across human cancers

(2013) Giovanni Ciriello et al.   NATURE GENETICS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

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

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

(2013) Ekta Khurana et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Frequency of TERT promoter mutations in human cancers

(2013) João Vinagre et al.   Nature Communications

Comprehensive identification of mutational cancer driver genes across 12 tumor types

(2013) David Tamborero et al.   Scientific Reports

The Genomic and Transcriptomic Landscape of a HeLa Cell Line

(2013) Jonathan J. M. Landry et al.   G3-Genes Genomes Genetics

RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State

(2013) Nisha Rajagopal et al.   PLoS Computational Biology

The Life History of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

(2012) J. O. Yanez-Cuna et al.   GENOME RESEARCH

Sequence and chromatin determinants of cell-type-specific transcription factor binding

(2012) A. Arvey et al.   GENOME RESEARCH

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes

(2012) D. U. Gorkin et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

(2012) A. P. Boyle et al.   GENOME RESEARCH

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

DNase I sensitivity QTLs are a major determinant of human expression variation

(2012) Jacob F. Degner et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

Breast cancer risk–associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression

(2012) Richard Cowper-Sal·lari et al.   NATURE GENETICS

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

ENCODE Data in the UCSC Genome Browser: year 5 update

(2012) Kate R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

Dissecting the regulatory architecture of gene expression QTLs

(2012) Daniel J Gaffney et al.   GENOME BIOLOGY

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Prospective Multicenter Phase II Trial of Systemic ADH-1 in Combination With Melphalan via Isolated Limb Infusion in Patients With Advanced Extremity Melanoma

(2011) Georgia M. Beasley et al.   JOURNAL OF CLINICAL ONCOLOGY

Improved accuracy of supervised CRM discovery with interpolated Markov models and cross-species comparison

(2011) Majid Kazemian et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Expression Profiling of Five Mouse Models Identifies Similarities and Differences with Human Psoriasis

(2011) William R. Swindell et al.   PLoS One

BigWig and BigBed: enabling browsing of large distributed datasets

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

Genome-wide discovery of human heart enhancers

(2010) L. Narlikar et al.   GENOME RESEARCH

Homotypic clusters of transcription factor binding sites are a key component of human promoters and enhancers

(2010) V. Gotea et al.   GENOME RESEARCH

Gene Expression Signatures as a Guide to Treatment Strategies for In-Transit Metastatic Melanoma

(2010) Christina K. Augustine et al.   MOLECULAR CANCER THERAPEUTICS

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

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

Genome-wide prediction of transcription factor binding sites using an integrated model

(2010) Kyoung-Jae Won et al.   GENOME BIOLOGY

Computational methods for the detection of cis-regulatory modules

(2009) P. Van Loo et al.   BRIEFINGS IN BIOINFORMATICS

Learning from Imbalanced Data

(2009) Haibo He et al.   IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING

Genome-wide scan reveals association of psoriasis with IL-23 and NF-κB pathways

(2009) Rajan P Nair et al.   NATURE GENETICS

The gene expression profiles of primary and metastatic melanoma yields a transition point of tumor progression and metastasis

(2008) Adam I Riker et al.   BMC Medical Genomics