Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome

Systematic analysis of binding of transcription factors to noncoding variants

(2021) Jian Yan et al.   NATURE

Integration of Multiple Epigenomic Marks Improves Prediction of Variant Impact in Saturation Mutagenesis Reporter Assay

(2019) Dustin Shigaki et al.   HUMAN MUTATION

Benefits and limitations of genome-wide association studies

(2019) Vivian Tam et al.   NATURE REVIEWS GENETICS

Predicting functional variants in enhancer and promoter elements using RegulomeDB

(2019) Shengcheng Dong et al.   HUMAN MUTATION

regBase: whole genome base-wise aggregation and functional prediction for human non-coding regulatory variants

(2019) Shijie Zhang et al.   NUCLEIC ACIDS RESEARCH

FUN-LDA: A Latent Dirichlet Allocation Model for Predicting Tissue-Specific Functional Effects of Noncoding Variation: Methods and Applications

(2018) Daniel Backenroth et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Direct Identification of Hundreds of Expression-Modulating Variants using a Multiplexed Reporter Assay

(2018) Ryan Tewhey et al.   CELL

Sequential regulatory activity prediction across chromosomes with convolutional neural networks

(2018) David R. Kelley et al.   GENOME RESEARCH

The NHGRI-EBI GWAS Catalog of published genome-wide association studies, targeted arrays and summary statistics 2019

(2018) Annalisa Buniello et al.   NUCLEIC ACIDS RESEARCH

A semi-supervised approach for predicting cell-type specific functional consequences of non-coding variation using MPRAs

(2018) Zihuai He et al.   Nature Communications

Predicting enhancer activity and variant impact using gkm-SVM

(2017) Michael A. Beer   HUMAN MUTATION

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Protein-altering and regulatory genetic variants near GATA4 implicated in bicuspid aortic valve

(2017) Bo Yang et al.   Nature Communications

DanQ: a hybrid convolutional and recurrent deep neural network for quantifying the function of DNA sequences

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

A uniform survey of allele-specific binding and expression over 1000-Genomes-Project individuals

(2016) Jieming Chen et al.   Nature Communications

Integrative Tissue-Specific Functional Annotations in the Human Genome Provide Novel Insights on Many Complex Traits and Improve Signal Prioritization in Genome Wide Association Studies

(2016) Qiongshi Lu et al.   PLoS Genetics

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

A global reference for human genetic variation

(2015) Richard A. Gibbs et al.   NATURE

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

(2015) Babak Alipanahi et al.   NATURE BIOTECHNOLOGY

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

(2015) Jian Zhou et al.   NATURE METHODS

HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease

(2015) Lucas D. Ward et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Martin Kircher et al.   NATURE GENETICS

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

(2013) P. Kheradpour et al.   GENOME RESEARCH

GWAS3D: detecting human regulatory variants by integrative analysis of genome-wide associations, chromosome interactions and histone modifications

(2013) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

Annotation of functional variation in personal genomes using RegulomeDB

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

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

(2012) Jacob F. Degner et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

AlleleSeq: analysis of allele-specific expression and binding in a network framework

(2011) J. Rozowsky et al.   Molecular Systems Biology

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

From noncoding variant to phenotype via SORT1 at the 1p13 cholesterol locus

(2010) Kiran Musunuru et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

High-Resolution Mapping and Characterization of Open Chromatin across the Genome

(2008) Alan P. Boyle et al.   CELL

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

(2008) Montgomery Slatkin   NATURE REVIEWS GENETICS