Published in Cell on November 17, 2016
Genetic-epigenetic interactions in cis: a major focus in the post-GWAS era. Genome Biol (2017) 0.75
Living in an adaptive world: Genomic dissection of the genus Homo and its immune response. J Exp Med (2017) 0.75
Concerted Genetic Function in Blood Traits. Cell (2016) 0.75
Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types. Genome Biol (2017) 0.75
Functional variation in allelic methylomes underscores a strong genetic contribution and reveals novel epigenetic alterations in the human epigenome. Genome Biol (2017) 0.75
Chromatin Remodeling Protein SMAR1 Is a Critical Regulator of T Helper Cell Differentiation and Inflammatory Diseases. Front Immunol (2017) 0.75
Translational Perspective on Epigenetics in Cardiovascular Disease. J Am Coll Cardiol (2017) 0.75
Immunogenomic approaches to understand the function of immune disease variants. Immunology (2017) 0.75
New "programmers" in tissue macrophage activation. Pflugers Arch (2017) 0.75
PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet (2007) 209.92
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet (2011) 59.36
Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A (2009) 54.68
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48
STAR: ultrafast universal RNA-seq aligner. Bioinformatics (2012) 25.21
Rapid and accurate haplotype phasing and missing-data inference for whole-genome association studies by use of localized haplotype clustering. Am J Hum Genet (2007) 24.68
Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics (2006) 22.61
GCTA: a tool for genome-wide complex trait analysis. Am J Hum Genet (2010) 20.73
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature (2012) 16.13
The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res (2013) 14.23
Efficient control of population structure in model organism association mapping. Genetics (2008) 12.32
Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet (2012) 11.09
Integrative analysis of 111 reference human epigenomes. Nature (2015) 10.32
A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics (2011) 8.19
Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet (2011) 7.98
ChromHMM: automating chromatin-state discovery and characterization. Nat Methods (2012) 7.66
DNA methylation age of human tissues and cell types. Genome Biol (2013) 7.48
Multiple common variants for celiac disease influencing immune gene expression. Nat Genet (2010) 6.90
Genetics of rheumatoid arthritis contributes to biology and drug discovery. Nature (2013) 6.57
The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet (2011) 5.95
Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics (2014) 5.93
Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature (2014) 5.22
SWAN: Subset-quantile within array normalization for illumina infinium HumanMethylation450 BeadChips. Genome Biol (2012) 4.99
Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet (2009) 4.72
Analysis of immune-related loci identifies 48 new susceptibility variants for multiple sclerosis. Nat Genet (2013) 4.62
The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics (2012) 4.48
Accurate discovery of expression quantitative trait loci under confounding from spurious and genuine regulatory hotspots. Genetics (2008) 3.66
Innate immune activity conditions the effect of regulatory variants upon monocyte gene expression. Science (2014) 3.16
The African Genome Variation Project shapes medical genetics in Africa. Nature (2014) 3.11
Removing batch effects in analysis of expression microarray data: an evaluation of six batch adjustment methods. PLoS One (2011) 2.89
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res (2013) 2.77
Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife (2013) 2.70
Genome-wide allele-specific analysis: insights into regulatory variation. Nat Rev Genet (2010) 2.68
Association analyses identify 38 susceptibility loci for inflammatory bowel disease and highlight shared genetic risk across populations. Nat Genet (2015) 2.59
Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res (2013) 2.19
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat Protoc (2012) 2.14
Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell (2015) 2.11
Orchestrated intron retention regulates normal granulocyte differentiation. Cell (2013) 2.06
Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nat Genet (2015) 2.04
From expression QTLs to personalized transcriptomics. Nat Rev Genet (2011) 1.94
Transcriptional diversity during lineage commitment of human blood progenitors. Science (2014) 1.93
Population Variation and Genetic Control of Modular Chromatin Architecture in Humans. Cell (2015) 1.85
Bayesian test for colocalisation between pairs of genetic association studies using summary statistics. PLoS Genet (2014) 1.71
RNA splicing is a primary link between genetic variation and disease. Science (2016) 1.61
Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia. Genome Biol (2013) 1.57
ASTALAVISTA: dynamic and flexible analysis of alternative splicing events in custom gene datasets. Nucleic Acids Res (2007) 1.52
WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Methods (2015) 1.45
Genetic association analyses implicate aberrant regulation of innate and adaptive immunity genes in the pathogenesis of systemic lupus erythematosus. Nat Genet (2015) 1.42
Detection and interpretation of shared genetic influences on 42 human traits. Nat Genet (2016) 1.32
Using the realized relationship matrix to disentangle confounding factors for the estimation of genetic variance components of complex traits. Genet Sel Evol (2010) 1.27
Enhancers: emerging roles in cell fate specification. EMBO Rep (2012) 1.23
Identification of genetic variants associated with alternative splicing using sQTLseekeR. Nat Commun (2014) 1.08
Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat Commun (2015) 1.03
The role of Tec family kinases in myeloid cells. Int Arch Allergy Immunol (2004) 1.00
Fine-mapping cellular QTLs with RASQUAL and ATAC-seq. Nat Genet (2015) 0.98
AHT-ChIP-seq: a completely automated robotic protocol for high-throughput chromatin immunoprecipitation. Genome Biol (2013) 0.96
Efficient set tests for the genetic analysis of correlated traits. Nat Methods (2015) 0.95
Essential roles for the Tec family kinases Tec and Btk in M-CSF receptor signaling pathways that regulate macrophage survival. J Immunol (2008) 0.92
Genomic modulators of gene expression in human neutrophils. Nat Commun (2015) 0.91
Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs. Mol Syst Biol (2014) 0.86
Statistical comparison of methods to estimate the error probability in short-read Illumina sequencing. J Bioinform Comput Biol (2010) 0.84
The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease. Cell (2016) 1.13
Genetic and environmental influences interact with age and sex in shaping the human methylome. Nat Commun (2016) 0.88
Common genetic variation drives molecular heterogeneity in human iPSCs. Nature (2017) 0.80
Non-CG DNA methylation is a biomarker for assessing endodermal differentiation capacity in pluripotent stem cells. Nat Commun (2016) 0.79
Epigenetic variation taking center stage in immunological research. Epigenomics (2017) 0.75