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

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

Ontogeny, distribution and potential roles of 5-hydroxymethylcytosine in human liver function

(2013) Maxim Ivanov et al.   GENOME BIOLOGY

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Mapping cis- and trans-regulatory effects across multiple tissues in twins

(2012) Elin Grundberg et al.   NATURE GENETICS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Unraveling the Regulatory Mechanisms Underlying Tissue-Dependent Genetic Variation of Gene Expression

(2012) Jingyuan Fu et al.   PLoS Genetics

Variants Affecting Exon Skipping Contribute to Complex Traits

(2012) Younghee Lee et al.   PLoS Genetics

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

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

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

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

(2011) Jason Ernst et al.   NATURE

Epigenome-wide association studies for common human diseases

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

Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation

(2011) Jason Gertz 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

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

(2011) Jordana T Bell et al.   GENOME BIOLOGY

Genetic Control of Individual Differences in Gene-Specific Methylation in Human Brain

(2010) Dandan Zhang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) William McLaren et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression

(2010) E. Lalonde et al.   GENOME RESEARCH

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Transcriptome genetics using second generation sequencing in a Caucasian population

(2010) Stephen B. Montgomery et al.   NATURE

Understanding mechanisms underlying human gene expression variation with RNA sequencing

(2010) Joseph K. Pickrell et al.   NATURE

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

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

(2010) Jason Ernst et al.   NATURE BIOTECHNOLOGY

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

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

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

(2010) J. Raphael Gibbs et al.   PLoS Genetics

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Copy number variants, diseases and gene expression

(2009) C. N. Henrichsen et al.   HUMAN MOLECULAR GENETICS

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

ENCODE whole-genome data in the UCSC Genome Browser

(2009) K. R. Rosenbloom et al.   NUCLEIC ACIDS RESEARCH

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

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Tissue Effect on Genetic Control of Transcript Isoform Variation

(2009) Tony Kwan et al.   PLoS Genetics

Fine-Scale Variation and Genetic Determinants of Alternative Splicing across Individuals

(2009) Jasmin Coulombe-Huntington et al.   PLoS Genetics

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

(2008) Alan P. Boyle et al.   CELL

Identification of common genetic variants that account for transcript isoform variation between human populations

(2008) Wei Zhang et al.   HUMAN GENETICS

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

From gene expression to disease risk

(2008) Emmanouil T Dermitzakis   NATURE GENETICS

Genome-wide analysis of transcript isoform variation in humans

(2008) Tony Kwan et al.   NATURE GENETICS

Tissue-Specific Genetic Control of Splicing: Implications for the Study of Complex Traits

(2008) Erin L Heinzen et al.   PLOS BIOLOGY

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

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