Principles and methods of in-silico prioritization of non-coding regulatory variants

An Upper Limit on the Functional Fraction of the Human Genome

(2017) Dan Graur   Genome Biology and Evolution

Reports from CAGI: The Critical Assessment of Genome Interpretation

(2017) Roger A Hoskins et al.   HUMAN MUTATION

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

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

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

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

The dark side of the human genome

(2016) Kelly Rae Chi   NATURE

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

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

Evolving insights into RNA modifications and their functional diversity in the brain

(2016) Sarah Nainar et al.   NATURE NEUROSCIENCE

Role of non-coding sequence variants in cancer

(2016) Ekta Khurana et al.   NATURE REVIEWS GENETICS

Genetic sources of population epigenomic variation

(2016) Aaron Taudt et al.   NATURE REVIEWS GENETICS

De Novo Synonymous Mutations in Regulatory Elements Contribute to the Genetic Etiology of Autism and Schizophrenia

(2016) Atsushi Takata et al.   NEURON

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

(2016) Daniel Quang et al.   NUCLEIC ACIDS RESEARCH

Deciphering ENCODE

(2016) Adam G. Diehl et al.   TRENDS IN GENETICS

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

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

(2015) Hashem A. Shihab et al.   BIOINFORMATICS

GREGOR: evaluating global enrichment of trait-associated variants in epigenomic features using a systematic, data-driven approach

(2015) Ellen M. Schmidt et al.   BIOINFORMATICS

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions

(2015) Fabian Grubert et al.   CELL

Population Variation and Genetic Control of Modular Chromatin Architecture in Humans

(2015) Sebastian M. Waszak et al.   CELL

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

(2015) Feng Zhang et al.   HUMAN MOLECULAR GENETICS

Paradigm shifts in genomics through the FANTOM projects

(2015) Michiel de Hoon et al.   MAMMALIAN GENOME

Deep learning

(2015) Yann LeCun 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

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

(2015) Dongwon Lee et al.   NATURE GENETICS

Automated, high-throughput derivation, characterization and differentiation of induced pluripotent stem cells

(2015) Daniel Paull et al.   NATURE METHODS

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

(2015) Jian Zhou et al.   NATURE METHODS

Psychiatric genome-wide association study analyses implicate neuronal, immune and histone pathways

(2015)   NATURE NEUROSCIENCE

The role of regulatory variation in complex traits and disease

(2015) Frank W. Albert et al.   NATURE REVIEWS GENETICS

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

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

Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing

(2015) Maria Gutierrez-Arcelus et al.   PLoS Genetics

Gateways to the FANTOM5 promoter level mammalian expression atlas

(2015) Marina Lizio et al.   GENOME BIOLOGY

Enlight: web-based integration of GWAS results with biological annotations

(2014) Y. Guo et al.   BIOINFORMATICS

Deep learning of the tissue-regulated splicing code

(2014) Michael K. K. Leung et al.   BIOINFORMATICS

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

(2014) Daniel Quang et al.   BIOINFORMATICS

Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples

(2014) Yew Lee et al.   BIOLOGICAL PROCEDURES ONLINE

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

Access to personalized medicine: factors influencing the use and value of gene expression profiling in breast cancer treatment

(2014) Y. Bombard et al.   Current Oncology

Genome-wide map of regulatory interactions in the human genome

(2014) Nastaran Heidari et al.   GENOME RESEARCH

Biological insights from 108 schizophrenia-associated genetic loci

(2014)   NATURE

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

(2014) Martin Kircher et al.   NATURE GENETICS

Analysis of hundreds of cis-regulatory landscapes at high resolution in a single, high-throughput experiment

(2014) Jim R Hughes et al.   NATURE GENETICS

Functional annotation of noncoding sequence variants

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

Gene expression analysis in RA: towards personalized medicine

(2014) A N Burska et al.   PHARMACOGENOMICS JOURNAL

Identification of genetic variants associated with alternative splicing using sQTLseekeR

(2014) Jean Monlong et al.   Nature Communications

Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features

(2014) Mahmoud Ghandi et al.   PLoS Computational Biology

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

(2014) Jaroslav Bendl et al.   PLoS Computational Biology

Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

(2014) Nicholas E. Banovich et al.   PLoS Genetics

8.2% of the Human Genome Is Constrained: Variation in Rates of Turnover across Functional Element Classes in the Human Lineage

(2014) Chris M. Rands et al.   PLoS Genetics

Epigenetic Modifications: Basic Mechanisms and Role in Cardiovascular Disease (2013 Grover Conference Series)

(2014) Joseph Loscalzo et al.   Pulmonary Circulation

Genetic and Epigenetic Regulation of Human lincRNA Gene Expression

(2013) Konstantin Popadin et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Global Analysis of DNA Methylation Variation in Adipose Tissue from Twins Reveals Links to Disease-Associated Variants in Distal Regulatory Elements

(2013) Elin Grundberg et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Beyond GWASs: Illuminating the Dark Road from Association to Function

(2013) Stacey L. Edwards et al.   AMERICAN JOURNAL OF HUMAN GENETICS

ChroMoS: an integrated web tool for SNP classification, prioritization and functional interpretation

(2013) M. Barenboim et al.   BIOINFORMATICS

Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals

(2013) A. Battle et al.   GENOME RESEARCH

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

IntOGen-mutations identifies cancer drivers across tumor types

(2013) Abel Gonzalez-Perez et al.   NATURE METHODS

rSNPBase: a database for curated regulatory SNPs

(2013) Liyuan Guo et al.   NUCLEIC ACIDS 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

Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription

(2013) H. Kilpinen et al.   SCIENCE

Identification of Genetic Variants That Affect Histone Modifications in Human Cells

(2013) G. McVicker et al.   SCIENCE

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

(2013) Ekta Khurana et al.   SCIENCE

A cross-population extended haplotype-based homozygosity score test to detect positive selection in genome-wide scans

(2013) Ruzong Fan et al.   Statistics and Its Interface

How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis

(2012) Mauno Vihinen   BMC GENOMICS

Genetic variant representation, annotation and prioritization in the post-GWAS era

(2012) Mulin Jun Li et al.   CELL RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

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

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

VariBench: A Benchmark Database for Variations

(2012) Preethy Sasidharan Nair et al.   HUMAN MUTATION

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

Chromatin marks identify critical cell types for fine mapping complex trait variants

(2012) Gosia Trynka et al.   NATURE GENETICS

FunciSNP: an R/bioconductor tool integrating functional non-coding data sets with genetic association studies to identify candidate regulatory SNPs

(2012) Simon G. Coetzee et al.   NUCLEIC ACIDS RESEARCH

Extent, Causes, and Consequences of Small RNA Expression Variation in Human Adipose Tissue

(2012) Leopold Parts et al.   PLoS Genetics

The diabetogenic VPS13C/C2CD4A/C2CD4B rs7172432 variant impairs glucose-stimulated insulin response in 5,722 non-diabetic Danish individuals

(2011) N. Grarup et al.   DIABETOLOGIA

A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression

(2011) Kevin C. Wang et al.   NATURE

Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs

(2011) Morgane Thomas-Chollier et al.   Nature Protocols

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

(2011) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

(2011) L. D. Ward et al.   NUCLEIC ACIDS RESEARCH

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

Widespread transcription at neuronal activity-regulated enhancers

(2010) Tae-Kyung Kim et al.   NATURE

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

A genome-wide association study in the Japanese population identifies susceptibility loci for type 2 diabetes at UBE2E2 and C2CD4A-C2CD4B

(2010) Toshimasa Yamauchi et al.   NATURE GENETICS

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

Five-Vertebrate ChIP-seq Reveals the Evolutionary Dynamics of Transcription Factor Binding

(2010) D. Schmidt et al.   SCIENCE

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

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

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Genetics in geographically structured populations: defining, estimating and interpreting FST

(2009) Kent E. Holsinger et al.   NATURE REVIEWS GENETICS

Reduced expression of the Kinesin-Associated Protein 3 (KIFAP3) gene increases survival in sporadic amyotrophic lateral sclerosis

(2009) J. E. Landers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimation of Pairwise Identity by Descent From Dense Genetic Marker Data in a Population Sample of Haplotypes

(2008) S. R. Browning   GENETICS