Published in Genome Res on April 12, 2004
Global variation in copy number in the human genome. Nature (2006) 57.50
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Highly conserved non-coding sequences are associated with vertebrate development. PLoS Biol (2004) 10.59
Determinants of cell- and gene-specific transcriptional regulation by the glucocorticoid receptor. PLoS Genet (2007) 3.24
Short blocks from the noncoding parts of the human genome have instances within nearly all known genes and relate to biological processes. Proc Natl Acad Sci U S A (2006) 2.10
Fast-evolving noncoding sequences in the human genome. Genome Biol (2007) 1.64
Constitutional rearrangement of the architectural factor HMGA2: a novel human phenotype including overgrowth and lipomas. Am J Hum Genet (2004) 1.51
Evolutionary constraints in conserved nongenic sequences of mammals. Genome Res (2005) 1.50
Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet (2007) 1.45
Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int J Biol Sci (2007) 1.29
Cis-regulatory evolution of chalcone-synthase expression in the genus Arabidopsis. Genetics (2006) 0.99
Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries. Genetics (2008) 0.95
Modeling chromosomes in mouse to explore the function of genes, genomic disorders, and chromosomal organization. PLoS Genet (2006) 0.95
Retroviral enhancer detection insertions in zebrafish combined with comparative genomics reveal genomic regulatory blocks - a fundamental feature of vertebrate genomes. Genome Biol (2007) 0.94
The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci (2013) 0.94
Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Res (2012) 0.89
Unravelling cis-regulatory elements in the genome of the smallest photosynthetic eukaryote: phylogenetic footprinting in Ostreococcus. J Mol Evol (2009) 0.84
Conservation anchors in the vertebrate genome. Genome Biol (2005) 0.82
Structural relationships between highly conserved elements and genes in vertebrate genomes. PLoS One (2008) 0.80
Silencing effect of Hominoid highly conserved non-coding sequences on embryonic brain development. Genome Biol Evol (2017) 0.75
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol (1980) 113.75
The sequence of the human genome. Science (2001) 101.55
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
PAML: a program package for phylogenetic analysis by maximum likelihood. Comput Appl Biosci (1997) 45.07
Comparative analyses of multi-species sequences from targeted genomic regions. Nature (2003) 13.31
Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-species sequence comparisons. Science (2000) 10.14
Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (2003) 9.93
Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome Res (1997) 8.49
Differences in the localization and morphology of chromosomes in the human nucleus. J Cell Biol (1999) 6.35
Active conservation of noncoding sequences revealed by three-way species comparisons. Genome Res (2000) 6.18
Conserved noncoding sequences are reliable guides to regulatory elements. Trends Genet (2000) 5.88
The dog genome: survey sequencing and comparative analysis. Science (2003) 5.84
Genomic strategies to identify mammalian regulatory sequences. Nat Rev Genet (2001) 5.78
Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature (2002) 5.38
Intronic sequences flanking alternatively spliced exons are conserved between human and mouse. Genome Res (2003) 5.01
MultiPipMaker and supporting tools: Alignments and analysis of multiple genomic DNA sequences. Nucleic Acids Res (2003) 4.97
A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell (2003) 4.85
SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res (2003) 4.17
Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science (2003) 3.77
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
The promise of comparative genomics in mammals. Science (1999) 3.67
Comparative genomics: genome-wide analysis in metazoan eukaryotes. Nat Rev Genet (2003) 3.45
Position effect in human genetic disease. Hum Mol Genet (1998) 3.02
Evolutionarily conserved sequences on human chromosome 21. Genome Res (2001) 2.95
Evolutionary conservation of chromosome territory arrangements in cell nuclei from higher primates. Proc Natl Acad Sci U S A (2002) 2.53
Comparison of five methods for finding conserved sequences in multiple alignments of gene regulatory regions. Nucleic Acids Res (1999) 2.19
Transvection effects in Drosophila. Annu Rev Genet (2002) 2.18
A test of translational selection at 'silent' sites in the human genome: base composition comparisons in alternatively spliced genes. Gene (2000) 1.75
Transcriptional enhancers can act in trans. Trends Genet (1990) 1.38
Nuclear organization in differentiating oligodendrocytes. J Cell Sci (2002) 1.15
Locating regions of differential variability in DNA and protein sequences. Genetics (1999) 1.12
Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
The Bioperl toolkit: Perl modules for the life sciences. Genome Res (2002) 58.63
The Pfam protein families database. Nucleic Acids Res (2002) 51.34
Patterns of somatic mutation in human cancer genomes. Nature (2007) 38.41
Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics (2005) 24.54
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
International network of cancer genome projects. Nature (2010) 20.35
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature (2009) 18.39
EnsMart: a generic system for fast and flexible access to biological data. Genome Res (2004) 17.64
Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res (2008) 15.69
A whole-genome association study of major determinants for host control of HIV-1. Science (2007) 15.19
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
Ensembl 2011. Nucleic Acids Res (2010) 14.68
The International Protein Index: an integrated database for proteomics experiments. Proteomics (2004) 14.67
Ensembl 2012. Nucleic Acids Res (2011) 14.55
Reactome: a knowledge base of biologic pathways and processes. Genome Biol (2007) 13.36
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res (2008) 12.72
Ensembl 2014. Nucleic Acids Res (2013) 12.62
Prepublication data sharing. Nature (2009) 12.24
Ensembl 2013. Nucleic Acids Res (2012) 11.70
Optimized design and assessment of whole genome tiling arrays. Bioinformatics (2007) 11.38
Common regulatory variation impacts gene expression in a cell type-dependent manner. Science (2009) 11.28
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res (2010) 11.23
Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med (2008) 10.88
Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
Mouse genomic variation and its effect on phenotypes and gene regulation. Nature (2011) 10.66
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics (2012) 9.68
Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
The BioPAX community standard for pathway data sharing. Nat Biotechnol (2010) 9.19
Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
The Reactome pathway knowledgebase. Nucleic Acids Res (2013) 8.56
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Enredo and Pecan: genome-wide mammalian consistency-based multiple alignment with paralogs. Genome Res (2008) 7.35
The Ensembl core software libraries. Genome Res (2004) 7.30
The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res (2007) 7.29
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Genome scan meta-analysis of schizophrenia and bipolar disorder, part II: Schizophrenia. Am J Hum Genet (2003) 6.63
Integrating biological data--the Distributed Annotation System. BMC Bioinformatics (2008) 6.56
The European Nucleotide Archive. Nucleic Acids Res (2010) 6.48
Challenges and standards in integrating surveys of structural variation. Nat Genet (2007) 6.05
Heritable individual-specific and allele-specific chromatin signatures in humans. Science (2010) 5.94
Genome analysis of the platypus reveals unique signatures of evolution. Nature (2008) 5.74
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
Efficient storage of high throughput DNA sequencing data using reference-based compression. Genome Res (2011) 5.60
Immunity-related genes and gene families in Anopheles gambiae. Science (2002) 5.47
Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature (2002) 5.38
Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res (2008) 5.21
The genomic basis of adaptive evolution in threespine sticklebacks. Nature (2012) 5.20
Genome-wide nucleotide-level mammalian ancestor reconstruction. Genome Res (2008) 5.12
Improvements to services at the European Nucleotide Archive. Nucleic Acids Res (2009) 5.00
A physical map of the mouse genome. Nature (2002) 4.97
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res (2008) 4.84
A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol (2011) 4.84
Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res (2012) 4.80
Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet (2005) 4.79
High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells. Genome Res (2010) 4.69
A database and API for variation, dense genotyping and resequencing data. BMC Bioinformatics (2010) 4.68
Pebble and rock band: heuristic resolution of repeats and scaffolding in the velvet short-read de novo assembler. PLoS One (2009) 4.60
Sense from sequence reads: methods for alignment and assembly. Nat Methods (2009) 4.44
Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity. Genome Res (2011) 4.43
Human chromosome 21 gene expression atlas in the mouse. Nature (2002) 4.36
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res (2007) 4.33
Locus Reference Genomic sequences: an improved basis for describing human DNA variants. Genome Med (2010) 4.19
The GENCODE pseudogene resource. Genome Biol (2012) 4.18
Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet (2007) 3.98
Conserved non-genic sequences - an unexpected feature of mammalian genomes. Nat Rev Genet (2005) 3.97
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
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res (2007) 3.84
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82