Published in Nature on March 10, 2010
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol (2012) 14.01
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
Annotation of functional variation in personal genomes using RegulomeDB. Genome Res (2012) 11.47
Widespread RNA and DNA sequence differences in the human transcriptome. Science (2011) 11.45
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Generation of isogenic pluripotent stem cells differing exclusively at two early onset Parkinson point mutations. Cell (2011) 6.56
DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines. Genome Biol (2011) 6.48
The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet (2011) 5.95
From RNA-seq reads to differential expression results. Genome Biol (2010) 5.77
Genome-wide meta-analysis identifies 56 bone mineral density loci and reveals 14 loci associated with risk of fracture. Nat Genet (2012) 5.48
Patterns of cis regulatory variation in diverse human populations. PLoS Genet (2012) 5.28
AlleleSeq: analysis of allele-specific expression and binding in a network framework. Mol Syst Biol (2011) 4.71
RAB7L1 interacts with LRRK2 to modify intraneuronal protein sorting and Parkinson's disease risk. Neuron (2013) 4.67
Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics (2010) 4.56
Common genetic variation in the HLA region is associated with late-onset sporadic Parkinson's disease. Nat Genet (2010) 4.47
Optimization of de novo transcriptome assembly from next-generation sequencing data. Genome Res (2010) 4.18
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome. Genome Res (2011) 4.09
Human genome sequencing in health and disease. Annu Rev Med (2012) 3.76
Removing technical variability in RNA-seq data using conditional quantile normalization. Biostatistics (2012) 3.74
Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet (2011) 3.73
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Sequencing technology does not eliminate biological variability. Nat Biotechnol (2011) 3.20
Noisy splicing drives mRNA isoform diversity in human cells. PLoS Genet (2010) 3.19
ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinformatics (2011) 3.12
RNA-Seq gene profiling--a systematic empirical comparison. PLoS One (2014) 3.03
A quantitative atlas of polyadenylation in five mammals. Genome Res (2012) 2.87
A benchmark for RNA-seq quantification pipelines. Genome Biol (2016) 2.78
Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals. Genome Res (2013) 2.77
Fast computation and applications of genome mappability. PLoS One (2012) 2.73
Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife (2013) 2.70
Meta-analysis identifies common variants associated with body mass index in east Asians. Nat Genet (2012) 2.70
Identification, replication, and functional fine-mapping of expression quantitative trait loci in primary human liver tissue. PLoS Genet (2011) 2.68
Genome-wide allele-specific analysis: insights into regulatory variation. Nat Rev Genet (2010) 2.68
Comparison of RNA-Seq and microarray in transcriptome profiling of activated T cells. PLoS One (2014) 2.67
Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol (2011) 2.61
The expanding scope of DNA sequencing. Nat Biotechnol (2012) 2.57
Identifying recent adaptations in large-scale genomic data. Cell (2013) 2.57
Integrative eQTL-based analyses reveal the biology of breast cancer risk loci. Cell (2013) 2.56
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotechnol (2013) 2.53
Dissecting the regulatory architecture of gene expression QTLs. Genome Biol (2012) 2.51
Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet (2012) 2.50
A powerful and flexible approach to the analysis of RNA sequence count data. Bioinformatics (2011) 2.49
Polymorphic cis- and trans-regulation of human gene expression. PLoS Biol (2010) 2.42
A survey of best practices for RNA-seq data analysis. Genome Biol (2016) 2.37
Variation and genetic control of protein abundance in humans. Nature (2013) 2.32
The importance of phase information for human genomics. Nat Rev Genet (2011) 2.25
The real cost of sequencing: higher than you think! Genome Biol (2011) 2.22
RNA editing in the human ENCODE RNA-seq data. Genome Res (2012) 2.18
Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses. Nat Protoc (2012) 2.14
Combinatorial effects of multiple enhancer variants in linkage disequilibrium dictate levels of gene expression to confer susceptibility to common traits. Genome Res (2013) 2.14
Robustly detecting differential expression in RNA sequencing data using observation weights. Nucleic Acids Res (2014) 2.10
Gene-gene and gene-environment interactions detected by transcriptome sequence analysis in twins. Nat Genet (2014) 2.05
RNA-sequence analysis of human B-cells. Genome Res (2011) 2.02
A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. Genome Res (2011) 2.00
Heritability and genomics of gene expression in peripheral blood. Nat Genet (2014) 2.00
Effects of sequence variation on differential allelic transcription factor occupancy and gene expression. Genome Res (2012) 1.99
Allele-specific DNA methylation: beyond imprinting. Hum Mol Genet (2010) 1.98
Completely phased genome sequencing through chromosome sorting. Proc Natl Acad Sci U S A (2010) 1.96
CTCF-Mediated Human 3D Genome Architecture Reveals Chromatin Topology for Transcription. Cell (2015) 1.94
Integrative approaches for large-scale transcriptome-wide association studies. Nat Genet (2016) 1.90
The human pancreatic islet transcriptome: expression of candidate genes for type 1 diabetes and the impact of pro-inflammatory cytokines. PLoS Genet (2012) 1.88
A pipeline for RNA-seq data processing and quality assessment. Bioinformatics (2011) 1.85
The origin, evolution, and functional impact of short insertion-deletion variants identified in 179 human genomes. Genome Res (2013) 1.83
A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet (2011) 1.83
Deterministic and stochastic allele specific gene expression in single mouse blastomeres. PLoS One (2011) 1.82
Pervasive haplotypic variation in the spliceo-transcriptome of the human major histocompatibility complex. Genome Res (2011) 1.80
Rare and common regulatory variation in population-scale sequenced human genomes. PLoS Genet (2011) 1.79
Tissue-specific effects of genetic and epigenetic variation on gene regulation and splicing. PLoS Genet (2015) 1.78
seeQTL: a searchable database for human eQTLs. Bioinformatics (2011) 1.72
DNA methylation profiles of human active and inactive X chromosomes. Genome Res (2011) 1.68
Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts. Genome Res (2010) 1.67
A genome-wide association study identifies new susceptibility loci for esophageal adenocarcinoma and Barrett's esophagus. Nat Genet (2013) 1.67
The transcriptome of equine peripheral blood mononuclear cells. PLoS One (2015) 1.65
Human disease-associated genetic variation impacts large intergenic non-coding RNA expression. PLoS Genet (2013) 1.59
RNA sequencing reveals the role of splicing polymorphisms in regulating human gene expression. Genome Res (2010) 1.58
Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome. Genome Res (2013) 1.58
Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Res (2011) 1.58
Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association. PLoS Genet (2014) 1.55
Reliable identification of genomic variants from RNA-seq data. Am J Hum Genet (2013) 1.55
Transcriptome characterization by RNA sequencing identifies a major molecular and clinical subdivision in chronic lymphocytic leukemia. Genome Res (2013) 1.51
Gene expression drives local adaptation in humans. Genome Res (2013) 1.50
Association analyses identify multiple new lung cancer susceptibility loci and their interactions with smoking in the Chinese population. Nat Genet (2012) 1.49
Assessment of the genetic basis of rosacea by genome-wide association study. J Invest Dermatol (2015) 1.48
Novel genetic locus implicated for HIV-1 acquisition with putative regulatory links to HIV replication and infectivity: a genome-wide association study. PLoS One (2015) 1.46
WASP: allele-specific software for robust molecular quantitative trait locus discovery. Nat Methods (2015) 1.45
svaseq: removing batch effects and other unwanted noise from sequencing data. Nucleic Acids Res (2014) 1.43
Relating CNVs to transcriptome data at fine resolution: assessment of the effect of variant size, type, and overlap with functional regions. Genome Res (2011) 1.42
Structural haplotypes and recent evolution of the human 17q21.31 region. Nat Genet (2012) 1.41
Epistatic selection between coding and regulatory variation in human evolution and disease. Am J Hum Genet (2011) 1.41
RNA-Seq and human complex diseases: recent accomplishments and future perspectives. Eur J Hum Genet (2012) 1.38
An atlas of the Epstein-Barr virus transcriptome and epigenome reveals host-virus regulatory interactions. Cell Host Microbe (2012) 1.38
HaploReg v4: systematic mining of putative causal variants, cell types, regulators and target genes for human complex traits and disease. Nucleic Acids Res (2015) 1.36
Genetic architecture of microRNA expression: implications for the transcriptome and complex traits. Am J Hum Genet (2012) 1.36
NPEBseq: nonparametric empirical bayesian-based procedure for differential expression analysis of RNA-seq data. BMC Bioinformatics (2013) 1.34
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res (2008) 157.44
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
RNA-seq: an assessment of technical reproducibility and comparison with gene expression arrays. Genome Res (2008) 62.07
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
A new multipoint method for genome-wide association studies by imputation of genotypes. Nat Genet (2007) 52.68
Stem cell transcriptome profiling via massive-scale mRNA sequencing. Nat Methods (2008) 31.04
A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science (2008) 29.99
Genetic analysis of genome-wide variation in human gene expression. Nature (2004) 27.28
Ensembl 2009. Nucleic Acids Res (2008) 25.38
Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet (2008) 24.51
Population genomics of human gene expression. Nat Genet (2007) 24.49
Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science (2007) 23.38
Genetics of gene expression and its effect on disease. Nature (2008) 21.35
Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution. Nature (2008) 18.84
Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27
Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
Genetic variants regulating ORMDL3 expression contribute to the risk of childhood asthma. Nature (2007) 14.43
Transcriptome sequencing to detect gene fusions in cancer. Nature (2009) 11.63
Discovery of expression QTLs using large-scale transcriptional profiling in human lymphocytes. Nat Genet (2007) 11.09
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res (2008) 10.10
High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet (2008) 9.68
Transcript length bias in RNA-seq data confounds systems biology. Biol Direct (2009) 8.53
Cis-acting regulatory variation in the human genome. Science (2004) 4.47
Digital RNA allelotyping reveals tissue-specific and allele-specific gene expression in human. Nat Methods (2009) 4.38
Identifiability of isoform deconvolution from junction arrays and RNA-Seq. Bioinformatics (2009) 4.32
Targeted screening of cis-regulatory variation in human haplotypes. Genome Res (2008) 3.10
Homozygosity and linkage disequilibrium. Genetics (2002) 3.04
A hierarchical Bayesian model for comparing transcriptomes at the individual transcript isoform level. Nucleic Acids Res (2009) 2.12
Complete alternative splicing events are bubbles in splicing graphs. J Comput Biol (2009) 1.78
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
A second generation human haplotype map of over 3.1 million SNPs. Nature (2007) 85.39
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Population genomics of human gene expression. Nat Genet (2007) 24.49
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Relative impact of nucleotide and copy number variation on gene expression phenotypes. Science (2007) 23.38
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27
Common variants near MC4R are associated with fat mass, weight and risk of obesity. Nat Genet (2008) 15.94
GENCODE: producing a reference annotation for ENCODE. Genome Biol (2006) 15.08
Long noncoding RNAs with enhancer-like function in human cells. Cell (2010) 13.00
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
Common regulatory variation impacts gene expression in a cell type-dependent manner. Science (2009) 11.28
High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet (2008) 9.68
Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89
Mapping cis- and trans-regulatory effects across multiple tissues in twins. Nat Genet (2012) 6.97
The architecture of gene regulatory variation across multiple human tissues: the MuTHER study. PLoS Genet (2011) 5.95
Patterns of cis regulatory variation in diverse human populations. PLoS Genet (2012) 5.28
Genetic analysis of human traits in vitro: drug response and gene expression in lymphoblastoid cell lines. PLoS Genet (2008) 5.08
Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature (2006) 5.06
Candidate causal regulatory effects by integration of expression QTLs with complex trait genetic associations. PLoS Genet (2010) 4.95
Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet (2005) 4.79
Genevar: a database and Java application for the analysis and visualization of SNP-gene associations in eQTL studies. Bioinformatics (2010) 4.56
Human chromosome 21 gene expression atlas in the mouse. Nature (2002) 4.36
Meta-analysis of genome-wide scans for human adult stature identifies novel Loci and associations with measures of skeletal frame size. PLoS Genet (2009) 4.24
An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
Epigenome-wide scans identify differentially methylated regions for age and age-related phenotypes in a healthy ageing population. PLoS Genet (2012) 4.05
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res (2005) 3.89
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci U S A (2003) 3.73
Genome variation and evolution of the malaria parasite Plasmodium falciparum. Nat Genet (2006) 3.68
Chromosome 21 and down syndrome: from genomics to pathophysiology. Nat Rev Genet (2004) 3.58
Breaking the waves: improved detection of copy number variation from microarray-based comparative genomic hybridization. Genome Biol (2007) 3.54
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Identification of an imprinted master trans regulator at the KLF14 locus related to multiple metabolic phenotypes. Nat Genet (2011) 3.20
Sequencing of Culex quinquefasciatus establishes a platform for mosquito comparative genomics. Science (2010) 3.18
SNP and haplotype mapping for genetic analysis in the rat. Nat Genet (2008) 2.96
Sex-stratified genome-wide association studies including 270,000 individuals show sexual dimorphism in genetic loci for anthropometric traits. PLoS Genet (2013) 2.83
A genome-wide association study of testicular germ cell tumor. Nat Genet (2009) 2.79
Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife (2013) 2.70
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science (2013) 2.66
Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories. Nat Biotechnol (2013) 2.53
Poly(ADP-ribose) polymerase 1 participates in the phase entrainment of circadian clocks to feeding. Cell (2010) 2.52
Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet (2013) 2.40
Genome-wide association study of migraine implicates a common susceptibility variant on 8q22.1. Nat Genet (2010) 2.35
Large-scale population study of human cell lines indicates that dosage compensation is virtually complete. PLoS Genet (2007) 2.27
Reshaping the gut microbiome with bacterial transplantation and antibiotic intake. Genome Res (2010) 2.21
Genome-wide association identifies nine common variants associated with fasting proinsulin levels and provides new insights into the pathophysiology of type 2 diabetes. Diabetes (2011) 2.21
The genetics of regulatory variation in the human genome. Hum Genomics (2005) 2.05
Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts. Genome Res (2012) 2.04
The functional impact of structural variation in humans. Trends Genet (2008) 2.03
Polymorphisms in the low-density lipoprotein receptor-related protein 5 (LRP5) gene are associated with variation in vertebral bone mass, vertebral bone size, and stature in whites. Am J Hum Genet (2004) 1.97
Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes. Hum Mol Genet (2005) 1.96
From expression QTLs to personalized transcriptomics. Nat Rev Genet (2011) 1.94
Genome-wide association study identifies a common variant associated with risk of endometrial cancer. Nat Genet (2011) 1.84
Using gene expression to investigate the genetic basis of complex disorders. Hum Mol Genet (2008) 1.82
Interoperability with Moby 1.0--it's better than sharing your toothbrush! Brief Bioinform (2008) 1.80
Rare and common regulatory variation in population-scale sequenced human genomes. PLoS Genet (2011) 1.79
Distinct clinical phenotypes associated with JAK2V617F reflect differential STAT1 signaling. Cancer Cell (2010) 1.78
An immune response network associated with blood lipid levels. PLoS Genet (2010) 1.74
From gene expression to disease risk. Nat Genet (2008) 1.69
Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts. Genome Res (2010) 1.67
Fast-evolving noncoding sequences in the human genome. Genome Biol (2007) 1.64
Gene expression levels are a target of recent natural selection in the human genome. Mol Biol Evol (2008) 1.63
Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome. Genome Res (2013) 1.58
Genetic control of gene expression in whole blood and lymphoblastoid cell lines is largely independent. Genome Res (2011) 1.58
From DNA to RNA to disease and back: the 'central dogma' of regulatory disease variation. Hum Genomics (2006) 1.56
A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res (2008) 1.50
The Brisbane Systems Genetics Study: genetical genomics meets complex trait genetics. PLoS One (2012) 1.49
Finding the missing honey bee genes: lessons learned from a genome upgrade. BMC Genomics (2014) 1.46
Complex haplotypes, copy number polymorphisms and coding variation in two recently divergent mouse strains. Nat Genet (2005) 1.42
Modifier effects between regulatory and protein-coding variation. PLoS Genet (2008) 1.42
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Functional variation and evolution of non-coding DNA. Curr Opin Genet Dev (2006) 1.37
Congruence of additive and non-additive effects on gene expression estimated from pedigree and SNP data. PLoS Genet (2013) 1.35
Gene expression changes with age in skin, adipose tissue, blood and brain. Genome Biol (2013) 1.34
Genomic variation and its impact on gene expression in Drosophila melanogaster. PLoS Genet (2012) 1.31
Extent, causes, and consequences of small RNA expression variation in human adipose tissue. PLoS Genet (2012) 1.28
Sharing and Specificity of Co-expression Networks across 35 Human Tissues. PLoS Comput Biol (2015) 1.27
The resolution of the genetics of gene expression. Hum Mol Genet (2009) 1.24
Independent and population-specific association of risk variants at the IRGM locus with Crohn's disease. Hum Mol Genet (2010) 1.21
Analysis of case-control association studies with known risk variants. Bioinformatics (2012) 1.20
Expression quantitative trait loci: present and future. Philos Trans R Soc Lond B Biol Sci (2013) 1.20
Gene finding in the chicken genome. BMC Bioinformatics (2005) 1.20
Functional targets of the monogenic diabetes transcription factors HNF-1alpha and HNF-4alpha are highly conserved between mice and humans. Diabetes (2009) 1.19