Published in Nature on October 12, 2011
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GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res (2011) 11.03
Integrative analysis of 111 reference human epigenomes. Nature (2015) 10.32
Architecture of the human regulatory network derived from ENCODE data. Nature (2012) 10.28
Rare and common variants: twenty arguments. Nat Rev Genet (2012) 6.67
The UCSC Genome Browser database: 2014 update. Nucleic Acids Res (2013) 6.54
Genetic architectures of psychiatric disorders: the emerging picture and its implications. Nat Rev Genet (2012) 5.99
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An encyclopedia of mouse DNA elements (Mouse ENCODE). Genome Biol (2012) 4.15
Chromatin organization is a major influence on regional mutation rates in human cancer cells. Nature (2012) 3.92
Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Res (2012) 3.80
RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease. Science (2014) 3.48
Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A (2014) 3.35
Comparative genomics reveals insights into avian genome evolution and adaptation. Science (2014) 3.01
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The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature (2014) 2.93
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol (2013) 2.84
Evidence of abundant purifying selection in humans for recently acquired regulatory functions. Science (2012) 2.81
Phylo: a citizen science approach for improving multiple sequence alignment. PLoS One (2012) 2.64
The expanding scope of DNA sequencing. Nat Biotechnol (2012) 2.57
Identifying recent adaptations in large-scale genomic data. Cell (2013) 2.57
Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci (2012) 2.52
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Molecular phylogenetics: principles and practice. Nat Rev Genet (2012) 2.08
Partitioning heritability by functional annotation using genome-wide association summary statistics. Nat Genet (2015) 2.05
Heritability and genomics of gene expression in peripheral blood. Nat Genet (2014) 2.00
Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Res (2013) 1.96
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication. Science (2014) 1.96
Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science (2014) 1.94
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res (2013) 1.78
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res (2014) 1.69
Genome-wide analysis in German shepherd dogs reveals association of a locus on CFA 27 with atopic dermatitis. PLoS Genet (2013) 1.69
Enhancer-promoter interactions are encoded by complex genomic signatures on looping chromatin. Nat Genet (2016) 1.64
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet (2013) 1.64
Lagging-strand replication shapes the mutational landscape of the genome. Nature (2015) 1.63
Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature (2015) 1.62
Human-chimpanzee differences in a FZD8 enhancer alter cell-cycle dynamics in the developing neocortex. Curr Biol (2015) 1.61
Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res (2011) 1.60
Genome-wide signatures of convergent evolution in echolocating mammals. Nature (2013) 1.59
Comparative genetics of longevity and cancer: insights from long-lived rodents. Nat Rev Genet (2014) 1.58
Genome of the Chinese tree shrew. Nat Commun (2013) 1.55
Transcriptional enhancers in development and disease. Genome Biol (2012) 1.52
Cooperativity and rapid evolution of cobound transcription factors in closely related mammals. Cell (2013) 1.52
Evidence of a paucity of genes that interact with the mitochondrion on the X in mammals. Genome Biol Evol (2012) 1.52
The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell (2013) 1.51
Multiple evidence strands suggest that there may be as few as 19,000 human protein-coding genes. Hum Mol Genet (2014) 1.51
DNA-dependent formation of transcription factor pairs alters their binding specificity. Nature (2015) 1.50
Comprehensive identification and analysis of human accelerated regulatory DNA. Genome Res (2015) 1.49
Bovine polledness--an autosomal dominant trait with allelic heterogeneity. PLoS One (2012) 1.48
Genomic and network patterns of schizophrenia genetic variation in human evolutionary accelerated regions. Mol Biol Evol (2015) 1.48
Enhancer evolution across 20 mammalian species. Cell (2015) 1.48
Natural selection and infectious disease in human populations. Nat Rev Genet (2014) 1.48
Minke whale genome and aquatic adaptation in cetaceans. Nat Genet (2013) 1.46
Disrupted auto-regulation of the spliceosomal gene SNRPB causes cerebro-costo-mandibular syndrome. Nat Commun (2014) 1.46
Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior. Cell (2016) 1.46
Enhancers: five essential questions. Nat Rev Genet (2013) 1.46
Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Res (2013) 1.45
Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data. Nat Genet (2017) 1.42
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res (2012) 1.40
Genomic and expression analyses of Tursiops truncatus T cell receptor gamma (TRG) and alpha/delta (TRA/TRD) loci reveal a similar basic public γδ repertoire in dolphin and human. BMC Genomics (2016) 1.39
Functional Translational Readthrough: A Systems Biology Perspective. PLoS Genet (2016) 1.39
Evaluating empirical bounds on complex disease genetic architecture. Nat Genet (2013) 1.37
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
Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm. Genome Res (2013) 1.33
Evolution of transcription factor binding in metazoans - mechanisms and functional implications. Nat Rev Genet (2014) 1.33
The Ensembl gene annotation system. Database (Oxford) (2016) 1.31
A method for calculating probabilities of fitness consequences for point mutations across the human genome. Nat Genet (2015) 1.27
MiRmap: comprehensive prediction of microRNA target repression strength. Nucleic Acids Res (2012) 1.27
miREvo: an integrative microRNA evolutionary analysis platform for next-generation sequencing experiments. BMC Bioinformatics (2012) 1.27
dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Nonsynonymous and Splice-Site SNVs. Hum Mutat (2016) 1.25
Comparative primate genomics: emerging patterns of genome content and dynamics. Nat Rev Genet (2014) 1.23
Local regulation of gene expression by lncRNA promoters, transcription and splicing. Nature (2016) 1.22
Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair. Nat Biotechnol (2013) 1.21
Rare variants in PPARG with decreased activity in adipocyte differentiation are associated with increased risk of type 2 diabetes. Proc Natl Acad Sci U S A (2014) 1.21
Widespread purifying selection on RNA structure in mammals. Nucleic Acids Res (2013) 1.18
Structural and functional annotation of the porcine immunome. BMC Genomics (2013) 1.16
Comparative genomics as a tool to understand evolution and disease. Genome Res (2013) 1.16
Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol (2014) 1.16
Whole-genome sequence-based analysis of thyroid function. Nat Commun (2015) 1.16
Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Res (2014) 1.15
Contributions of protein-coding and regulatory change to adaptive molecular evolution in murid rodents. PLoS Genet (2013) 1.13
Phenotypic complementation of genetic immunodeficiency by chronic herpesvirus infection. Elife (2015) 1.13
Genome-wide analyses implicate 33 loci in heritable dog osteosarcoma, including regulatory variants near CDKN2A/B. Genome Biol (2013) 1.12
A field guide to whole-genome sequencing, assembly and annotation. Evol Appl (2014) 1.12
Advances in genome editing technology and its promising application in evolutionary and ecological studies. Gigascience (2014) 1.11
Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong? Mol Biol Evol (2013) 1.11
Next-generation sequencing-based molecular diagnosis of 82 retinitis pigmentosa probands from Northern Ireland. Hum Genet (2014) 1.10
Convergent evolution of the genomes of marine mammals. Nat Genet (2015) 1.10
Determinants of the rate of protein sequence evolution. Nat Rev Genet (2015) 1.09
P-value-based regulatory motif discovery using positional weight matrices. Genome Res (2012) 1.09
Dolphin genome provides evidence for adaptive evolution of nervous system genes and a molecular rate slowdown. Proc Biol Sci (2012) 1.09
Latent regulatory potential of human-specific repetitive elements. Mol Cell (2012) 1.08
Patterns of positive selection in seven ant genomes. Mol Biol Evol (2014) 1.08
8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage. PLoS Genet (2014) 1.08
Using genomics to characterize evolutionary potential for conservation of wild populations. Evol Appl (2014) 1.07
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
A map of human genome variation from population-scale sequencing. Nature (2010) 121.13
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Alternative isoform regulation in human tissue transcriptomes. Nature (2008) 52.76
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
Ultraconserved elements in the human genome. Science (2004) 17.14
Genetic mapping in human disease. Science (2008) 15.12
GENCODE: producing a reference annotation for ENCODE. Genome Biol (2006) 15.08
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90
Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66
Discovery and characterization of chromatin states for systematic annotation of the human genome. Nat Biotechnol (2010) 9.84
Identifying a high fraction of the human genome to be under selective constraint using GERP++. PLoS Comput Biol (2010) 8.69
Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A (2005) 8.15
Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci U S A (2007) 8.00
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Five-vertebrate ChIP-seq reveals the evolutionary dynamics of transcription factor binding. Science (2010) 7.41
Genome 10K: a proposal to obtain whole-genome sequence for 10,000 vertebrate species. J Hered (2009) 7.18
Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol (2006) 6.73
Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nat Genet (2007) 6.63
Reliable prediction of regulator targets using 12 Drosophila genomes. Genome Res (2007) 4.89
Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet (2005) 4.79
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes. Genome Res (2007) 4.73
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics (2011) 4.50
Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics (2009) 4.30
Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev (2009) 4.20
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A (2007) 4.11
Human-specific gain of function in a developmental enhancer. Science (2008) 3.84
Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res (2003) 3.52
Forces shaping the fastest evolving regions in the human genome. PLoS Genet (2006) 3.32
The share of human genomic DNA under selection estimated from human-mouse genomic alignments. Cold Spring Harb Symp Quant Biol (2003) 2.83
2-D structure of the A region of Xist RNA and its implication for PRC2 association. PLoS Biol (2010) 2.30
Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters. Genome Res (2007) 2.12
Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes. Genome Res (2011) 1.91
Massive turnover of functional sequence in human and other mammalian genomes. Genome Res (2010) 1.89
Targeted discovery of novel human exons by comparative genomics. Genome Res (2007) 1.79
Evidence of abundant stop codon readthrough in Drosophila and other metazoa. Genome Res (2011) 1.60
Genome-wide association study reveals multiple loci associated with primary tooth development during infancy. PLoS Genet (2010) 1.40
New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes. Genome Res (2011) 1.32
Error and error mitigation in low-coverage genome assemblies. PLoS One (2011) 1.31
A regulatory module embedded in the coding region of Hoxa2 controls expression in rhombomere 2. Proc Natl Acad Sci U S A (2008) 1.30
L-methionine availability regulates expression of the methionine adenosyltransferase 2A gene in human hepatocarcinoma cells: role of S-adenosylmethionine. J Biol Chem (2003) 1.29
Assisted assembly: how to improve a de novo genome assembly by using related species. Genome Biol (2009) 1.28
An ultraconserved Hox-Pbx responsive element resides in the coding sequence of Hoxa2 and is active in rhombomere 4. Nucleic Acids Res (2008) 1.22
The human genome browser at UCSC. Genome Res (2002) 168.23
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
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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
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
The complete genome of an individual by massively parallel DNA sequencing. Nature (2008) 52.81
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
The Pfam protein families database. Nucleic Acids Res (2002) 51.34
The structure of haplotype blocks in the human genome. Science (2002) 50.88
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
An obesity-associated gut microbiome with increased capacity for energy harvest. Nature (2006) 44.35
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Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell (2010) 39.09
Patterns of somatic mutation in human cancer genomes. Nature (2007) 38.41
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature (2008) 38.13
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Human-mouse alignments with BLASTZ. Genome Res (2003) 35.49
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
EGF receptor gene mutations are common in lung cancers from "never smokers" and are associated with sensitivity of tumors to gefitinib and erlotinib. Proc Natl Acad Sci U S A (2004) 33.85