Interpreting noncoding genetic variation in complex traits and human disease

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes

(2012) Rui Chen et al.   CELL

Linking disease associations with regulatory information in the human genome

(2012) M. A. Schaub et al.   GENOME RESEARCH

Annotation of functional variation in personal genomes using RegulomeDB

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

Plasma HDL cholesterol and risk of myocardial infarction: a mendelian randomisation study

(2012) Benjamin F Voight et al.   LANCET

The changes that count

(2012) Monya Baker   NATURE

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

(2012) Jacob F. Degner et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Architecture of the human regulatory network derived from ENCODE data

(2012) Mark B. Gerstein et al.   NATURE

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

(2012) Alexandre Melnikov et al.   NATURE BIOTECHNOLOGY

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

(2012) Eilon Sharon et al.   NATURE BIOTECHNOLOGY

Massively parallel functional dissection of mammalian enhancers in vivo

(2012) Rupali P Patwardhan et al.   NATURE BIOTECHNOLOGY

BLUEPRINT to decode the epigenetic signature written in blood

(2012) David Adams et al.   NATURE BIOTECHNOLOGY

Asking for more

(2012)   NATURE GENETICS

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

Bayesian inference analyses of the polygenic architecture of rheumatoid arthritis

(2012) Eli A Stahl et al.   NATURE GENETICS

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

An Abundance of Rare Functional Variants in 202 Drug Target Genes Sequenced in 14,002 People

(2012) M. R. Nelson et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

A Systematic Survey of Loss-of-Function Variants in Human Protein-Coding Genes

(2012) D. G. MacArthur et al.   SCIENCE

The Predictive Capacity of Personal Genome Sequencing

(2012) N. J. Roberts et al.   Science Translational Medicine

A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci

(2012) James G D Prendergast et al.   Epigenetics & Chromatin

Digital Epidemiology

(2012) Marcel Salathé et al.   PLoS Computational Biology

Transcriptional enhancers in development and disease

(2012) Noboru Sakabe et al.   GENOME BIOLOGY

Six Degrees of Epistasis: Statistical Network Models for GWAS

(2012) B. A. McKinney et al.   Frontiers in Genetics

Epistatic Selection between Coding and Regulatory Variation in Human Evolution and Disease

(2011) Tuuli Lappalainen et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Comprehensive Genome-wide Protein-DNA Interactions Detected at Single-Nucleotide Resolution

(2011) Ho Sung Rhee et al.   CELL

The Emerging Role of Electronic Medical Records in Pharmacogenomics

(2011) R A Wilke et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Statistical analysis of rare sequence variants: an overview of collapsing methods

(2011) Carmen Dering et al.   GENETIC EPIDEMIOLOGY

From Galton to GWAS: quantitative genetics of human height

(2011) PETER M. VISSCHER et al.   Genetics Research

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

Genetic risk prediction in complex disease

(2011) Luke Jostins et al.   HUMAN MOLECULAR GENETICS

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

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

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Initial impact of the sequencing of the human genome

(2011) Eric S. Lander   NATURE

Mapping and analysis of chromatin state dynamics in nine human cell types

(2011) Jason Ernst et al.   NATURE

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns

(2011) Sam John et al.   NATURE GENETICS

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

Family-based designs for genome-wide association studies

(2011) Jurg Ott et al.   NATURE REVIEWS GENETICS

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

Using Functional Annotation for the Empirical Determination of Bayes Factors for Genome-Wide Association Study Analysis

(2011) Jo Knight et al.   PLoS One

Epigenome characterization at single base-pair resolution

(2011) J. G. Henikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Classic Selective Sweeps Were Rare in Recent Human Evolution

(2011) R. D. Hernandez et al.   SCIENCE

The Importance of Synthetic Associations Will Only Be Resolved Empirically

(2011) David B. Goldstein   PLOS BIOLOGY

Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts

(2011) Francisco S. Roque et al.   PLoS Computational Biology

Construction and Analysis of an Integrated Regulatory Network Derived from High-Throughput Sequencing Data

(2011) Chao Cheng et al.   PLoS Computational Biology

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

(2011) Alexandra C. Nica et al.   PLoS Genetics

Prioritizing GWAS Results: A Review of Statistical Methods and Recommendations for Their Application

(2010) Rita M. Cantor et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genomics of Long-Range Regulatory Elements

(2010) James P. Noonan et al.   Annual Review of Genomics and Human Genetics

Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor

(2010) William McLaren et al.   BIOINFORMATICS

MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes

(2010) Yun Li et al.   GENETIC EPIDEMIOLOGY

Massive turnover of functional sequence in human and other mammalian genomes

(2010) S. Meader et al.   GENOME RESEARCH

An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer

(2010) N. F. Wasserman et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Functional analysis of CDKN2A/p16INK4a 5′-UTR variants predisposing to melanoma

(2010) Alessandra Bisio et al.   HUMAN MOLECULAR GENETICS

Analysis of SNPs with an effect on gene expression identifies UBE2L3 and BCL3 as potential new risk genes for Crohn's disease

(2010) Karin Fransen et al.   HUMAN MOLECULAR GENETICS

Epigenetics as a unifying principle in the aetiology of complex traits and diseases

(2010) Arturas Petronis   NATURE

Has the revolution arrived?

(2010) Francis Collins   NATURE

Deciphering the splicing code

(2010) Yoseph Barash et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

Hundreds of variants clustered in genomic loci and biological pathways affect human height

(2010) Hana Lango Allen et al.   NATURE

A map of human genome variation from population-scale sequencing

(2010) Richard M. Durbin et al.   NATURE

Discovery and characterization of chromatin states for systematic annotation of the human genome

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Common SNPs explain a large proportion of the heritability for human height

(2010) Jian Yang et al.   NATURE GENETICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Analysing biological pathways in genome-wide association studies

(2010) Kai Wang et al.   NATURE REVIEWS GENETICS

Statistical analysis strategies for association studies involving rare variants

(2010) Vikas Bansal et al.   NATURE REVIEWS GENETICS

Uncovering the roles of rare variants in common disease through whole-genome sequencing

(2010) Elizabeth T. Cirulli et al.   NATURE REVIEWS GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Variation in Transcription Factor Binding Among Humans

(2010) M. Kasowski et al.   SCIENCE

A Composite of Multiple Signals Distinguishes Causal Variants in Regions of Positive Selection

(2010) S. R. Grossman et al.   SCIENCE

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

(2010) D. Schmidt et al.   SCIENCE

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE

(2010) et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

The study of eQTL variations by RNA-seq: from SNPs to phenotypes

(2010) Jacek Majewski et al.   TRENDS IN 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

Common Inherited Variation in Mitochondrial Genes Is Not Enriched for Associations with Type 2 Diabetes or Related Glycemic Traits

(2010) Ayellet V. Segrè et al.   PLoS Genetics

Candidate Causal Regulatory Effects by Integration of Expression QTLs with Complex Trait Genetic Associations

(2010) Alexandra C. Nica et al.   PLoS Genetics

Trait-Associated SNPs Are More Likely to Be eQTLs: Annotation to Enhance Discovery from GWAS

(2010) Dan L. Nicolae et al.   PLoS Genetics

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

RNA and Disease

(2009) Thomas A. Cooper et al.   CELL

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Using biological networks to search for interacting loci in genome-wide association studies

(2009) Mathieu Emily et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

An agenda for personalized medicine

(2009) Pauline C. Ng et al.   NATURE

Finding the missing heritability of complex diseases

(2009) Teri A. Manolio et al.   NATURE

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Genomic views of distant-acting enhancers

(2009) Axel Visel et al.   NATURE

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

The 8q24 cancer risk variant rs6983267 shows long-range interaction with MYC in colorectal cancer

(2009) Mark M Pomerantz et al.   NATURE GENETICS

Global patterns of cis variation in human cells revealed by high-density allelic expression analysis

(2009) Bing Ge et al.   NATURE GENETICS

The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling

(2009) Sari Tuupanen et al.   NATURE GENETICS

Global mapping of protein-DNA interactions in vivo by digital genomic footprinting

(2009) Jay R Hesselberth et al.   NATURE METHODS

Detecting gene–gene interactions that underlie human diseases

(2009) Heather J Cordell   NATURE REVIEWS GENETICS

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Genetic Risk Prediction — Are We There Yet?

(2009) Peter Kraft et al.   NEW ENGLAND JOURNAL OF MEDICINE

Potential etiologic and functional implications of genome-wide association loci for human diseases and traits

(2009) L. A. Hindorff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

A Genome-Wide Association Study Identifies Novel and Functionally Related Susceptibility Loci for Kawasaki Disease

(2009) David Burgner et al.   PLoS Genetics

Identifying Relationships among Genomic Disease Regions: Predicting Genes at Pathogenic SNP Associations and Rare Deletions

(2009) Soumya Raychaudhuri et al.   PLoS Genetics

The Role of Geography in Human Adaptation

(2009) Graham Coop et al.   PLoS Genetics

The promise and reality of personal genomics

(2009) Bryndis Yngvadottir et al.   GENOME BIOLOGY

A Combinatorial Approach to Detecting Gene-Gene and Gene-Environment Interactions in Family Studies

(2008) Xiang-Yang Lou et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Polymorphism Interaction Analysis (PIA): a method for investigating complex gene-gene interactions

(2008) Leah E Mechanic et al.   BMC BIOINFORMATICS

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

(2008) Alan P. Boyle et al.   CELL

From Human Genetics and Genomics to Pharmacogenetics and Pharmacogenomics: Past Lessons, Future Directions

(2008) Daniel W. Nebert et al.   DRUG METABOLISM REVIEWS

Exploiting the proteome to improve the genome-wide genetic analysis of epistasis in common human diseases

(2008) Kristine A. Pattin et al.   HUMAN GENETICS

Association Mapping of Complex Diseases with Ancestral Recombination Graphs: Models and Efficient Algorithms

(2008) Yufeng Wu   JOURNAL OF COMPUTATIONAL BIOLOGY

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

Genomic surveys by methylation-sensitive SNP analysis identify sequence-dependent allele-specific DNA methylation

(2008) Kristi Kerkel et al.   NATURE GENETICS

Integrating large-scale functional genomic data to dissect the complexity of yeast regulatory networks

(2008) Jun Zhu et al.   NATURE GENETICS

Integrated genotype calling and association analysis of SNPs, common copy number polymorphisms and rare CNVs

(2008) Joshua M Korn et al.   NATURE GENETICS

Genome-wide association studies for complex traits: consensus, uncertainty and challenges

(2008) Mark I. McCarthy et al.   NATURE REVIEWS GENETICS

Genetic architecture of complex traits: Large phenotypic effects and pervasive epistasis

(2008) H. Shao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

(2008) Z. Wang et al.   RNA

The Repertoire and Dynamics of Evolutionary Adaptations to Controlled Nutrient-Limited Environments in Yeast

(2008) David Gresham et al.   PLoS Genetics

High-Resolution Mapping of Expression-QTLs Yields Insight into Human Gene Regulation

(2008) Jean-Baptiste Veyrieras et al.   PLoS Genetics

Resolving Individuals Contributing Trace Amounts of DNA to Highly Complex Mixtures Using High-Density SNP Genotyping Microarrays

(2008) Nils Homer et al.   PLoS Genetics

Data and Theory Point to Mainly Additive Genetic Variance for Complex Traits

(2008) William G. Hill et al.   PLoS Genetics

Mendelian randomization: Using genes as instruments for making causal inferences in epidemiology

(2007) Debbie A. Lawlor et al.   STATISTICS IN MEDICINE