Predicting effects of noncoding variants with deep learning–based sequence model

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

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

(2015) Dongwon Lee et al.   NATURE GENETICS

GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database

(2014) R. Leslie et al.   BIOINFORMATICS

A general framework for estimating the relative pathogenicity of human genetic variants

(2014) Martin Kircher et al.   NATURE GENETICS

Functional annotation of noncoding sequence variants

(2014) Graham R S Ritchie et al.   NATURE METHODS

Predicting the human epigenome from DNA motifs

(2014) John W Whitaker et al.   NATURE METHODS

Transcription factor binding predicts histone modifications in human cell lines

(2014) Dan Benveniste et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

The Human Gene Mutation Database: building a comprehensive mutation repository for clinical and molecular genetics, diagnostic testing and personalized genomic medicine

(2013) Peter D. Stenson et al.   HUMAN GENETICS

Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

(2013) Michael N Weedon et al.   NATURE GENETICS

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

The UCSC Genome Browser database: 2014 update

(2013) Donna Karolchik et al.   NUCLEIC ACIDS RESEARCH

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

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

(2012) A. Arvey et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

An expansive human regulatory lexicon encoded in transcription factor footprints

(2012) Shane Neph et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

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

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

Detection of nonneutral substitution rates on mammalian phylogenies

(2009) K. S. Pollard et al.   GENOME RESEARCH