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

Biological relevance of computationally predicted pathogenicity of noncoding variants

(2019) Li Liu et al.   Nature Communications

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk

(2019) Jian Zhou et al.   NATURE GENETICS

The Post-GWAS Era: From Association to Function

(2018) Michael D. Gallagher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

A benchmark study of scoring methods for non-coding mutations

(2018) Damien Drubay et al.   BIOINFORMATICS

Regulatory variants: from detection to predicting impact

(2018) Elena Rojano et al.   BRIEFINGS IN BIOINFORMATICS

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

(2018) Ryan Tewhey et al.   CELL

The human noncoding genome defined by genetic diversity

(2018) Julia di Iulio et al.   NATURE GENETICS

A global transcriptional network connecting noncoding mutations to changes in tumor gene expression

(2018) Wei Zhang et al.   NATURE GENETICS

IW-Scoring: an Integrative Weighted Scoring framework for annotating and prioritizing genetic variations in the noncoding genome

(2018) Jun Wang et al.   NUCLEIC ACIDS RESEARCH

GWAS4D: multidimensional analysis of context-specific regulatory variant for human complex diseases and traits

(2018) Dandan Huang et al.   NUCLEIC ACIDS RESEARCH

Modified penetrance of coding variants by cis-regulatory variation contributes to disease risk

(2018) Stephane E. Castel et al.   NATURE GENETICS

CADD: predicting the deleteriousness of variants throughout the human genome

(2018) Philipp Rentzsch et al.   NUCLEIC ACIDS 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

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Fine-mapping inflammatory bowel disease loci to single-variant resolution

(2017) Hailiang Huang et al.   NATURE

The impact of rare variation on gene expression across tissues

(2017) Xin Li et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data

(2017) Yi-Fei Huang et al.   NATURE GENETICS

mTCTScan: a comprehensive platform for annotation and prioritization of mutations affecting drug sensitivity in cancers

(2017) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

ClinVar: improving access to variant interpretations and supporting evidence

(2017) Melissa J Landrum et al.   NUCLEIC ACIDS RESEARCH

Mining the Unknown: Assigning Function to Noncoding Single Nucleotide Polymorphisms

(2017) Sierra S. Nishizaki et al.   TRENDS IN GENETICS

Functional dissection of breast cancer risk-associated TERT promoter variants

(2017) Sonja Helbig et al.   Oncotarget

CScape: a tool for predicting oncogenic single-point mutations in the cancer genome

(2017) Mark F. Rogers et al.   Scientific Reports

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease

(2016) Damian Smedley et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Predicting regulatory variants with composite statistic

(2016) Mulin Jun Li et al.   BIOINFORMATICS

Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits

(2016) Jacob C. Ulirsch et al.   CELL

Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks

(2016) David R. Kelley et al.   GENOME RESEARCH

Regulatory Single-Nucleotide Variant Predictor Increases Predictive Performance of Functional Regulatory Variants

(2016) Thomas A. Peterson et al.   HUMAN MUTATION

dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs

(2016) Xiaoming Liu et al.   HUMAN MUTATION

Understanding TERT Promoter Mutations: A Common Path to Immortality

(2016) R. J. A. Bell et al.   MOLECULAR CANCER RESEARCH

High-throughput mapping of regulatory DNA

(2016) Nisha Rajagopal et al.   NATURE BIOTECHNOLOGY

A spectral approach integrating functional genomic annotations for coding and noncoding variants

(2016) Iuliana Ionita-Laza et al.   NATURE GENETICS

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

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

An integrative approach to predicting the functional effects of non-coding and coding sequence variation

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

Genetic Variation Determines PPARγ Function and Anti-diabetic Drug Response In Vivo

(2015) Raymond E. Soccio et al.   CELL

Non-coding genetic variants in human disease: Figure 1.

(2015) Feng Zhang et al.   HUMAN MOLECULAR 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

A method for calculating probabilities of fitness consequences for point mutations across the human genome

(2015) Brad Gulko et al.   NATURE GENETICS

Running spell-check to identify regulatory variants

(2015) Martin Kircher et al.   NATURE GENETICS

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo

(2015) Matthew T Maurano et al.   NATURE GENETICS

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

(2015) Dongwon Lee et al.   NATURE GENETICS

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

(2015) Jian Zhou et al.   NATURE METHODS

Prognostic quality of activating TERT promoter mutations in glioblastoma: interaction with the rs2853669 polymorphism and patient age at diagnosis

(2015) Sabine Spiegl-Kreinecker et al.   NEURO-ONCOLOGY

GWASdb v2: an update database for human genetic variants identified by genome-wide association studies

(2015) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

ORegAnno 3.0: a community-driven resource for curated regulatory annotation

(2015) Robert Lesurf et al.   NUCLEIC ACIDS RESEARCH

A Statistical Framework to Predict Functional Non-Coding Regions in the Human Genome Through Integrated Analysis of Annotation Data

(2015) Qiongshi Lu et al.   Scientific Reports

DANN: a deep learning approach for annotating the pathogenicity of genetic variants

(2014) Daniel Quang et al.   BIOINFORMATICS

Exploring the function of genetic variants in the non-coding genomic regions: approaches for identifying human regulatory variants affecting gene expression

(2014) M. J. Li et al.   BRIEFINGS IN BIOINFORMATICS

Identifying Causal Variants at Loci with Multiple Signals of Association

(2014) F. Hormozdiari et al.   GENETICS

Genetic and epigenetic fine mapping of causal autoimmune disease variants

(2014) Kyle Kai-How Farh et al.   NATURE

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

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

TERT promoter mutations in bladder cancer affect patient survival and disease recurrence through modification by a common polymorphism

(2013) P. S. Rachakonda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Ekta Khurana et al.   SCIENCE

Integrative Modeling of eQTLs and Cis-Regulatory Elements Suggests Mechanisms Underlying Cell Type Specificity of eQTLs

(2013) Christopher D. Brown et al.   PLoS Genetics

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

Tabix: fast retrieval of sequence features from generic TAB-delimited files

(2011) H. Li   BIOINFORMATICS

LocusZoom: regional visualization of genome-wide association scan results

(2010) R. J. Pruim et al.   BIOINFORMATICS

Detection of nonneutral substitution rates on mammalian phylogenies

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

High-resolution analysis of DNA regulatory elements by synthetic saturation mutagenesis

(2009) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY