Published in Mamm Genome on October 01, 2002
Regulatory polymorphisms underlying complex disease traits. J Mol Med (Berl) (2004) 3.22
Variation in conserved non-coding sequences on chromosome 5q and susceptibility to asthma and atopy. Respir Res (2005) 0.88
Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics (2003) 100.88
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res (2003) 52.74
Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation. Nucleic Acids Res (2002) 40.03
Integrated genomic analysis identifies clinically relevant subtypes of glioblastoma characterized by abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell (2010) 39.09
GOstat: find statistically overrepresented Gene Ontologies within a group of genes. Bioinformatics (2004) 30.14
Comparative metagenomics of microbial communities. Science (2005) 25.88
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
International network of cancer genome projects. Nature (2010) 20.35
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature (2004) 20.20
ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
The Sorghum bicolor genome and the diversification of grasses. Nature (2009) 14.62
The integrated microbial genomes (IMG) system in 2007: data content and analysis tool extensions. Nucleic Acids Res (2007) 13.81
VISTA: computational tools for comparative genomics. Nucleic Acids Res (2004) 13.52
IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy. Nat Genet (2009) 13.03
The Chlamydomonas genome reveals the evolution of key animal and plant functions. Science (2007) 11.15
In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60
A genotype calling algorithm for affymetrix SNP arrays. Bioinformatics (2005) 10.43
AVID: A global alignment program. Genome Res (2003) 10.06
Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (2003) 9.93
Scanning human gene deserts for long-range enhancers. Science (2003) 9.75
Insights into the phylogeny and coding potential of microbial dark matter. Nature (2013) 8.55
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
Sequencing and analysis of Neanderthal genomic DNA. Science (2006) 8.06
The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet (2005) 7.65
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
The integrated microbial genomes (IMG) system. Nucleic Acids Res (2006) 7.34
rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res (2002) 7.33
IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res (2007) 7.18
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res (2006) 7.04
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science (2011) 6.93
Visualizing genomes: techniques and challenges. Nat Methods (2010) 6.66
Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol (2008) 6.30
Genomic views of distant-acting enhancers. Nature (2009) 6.27
A benchmark for Affymetrix GeneChip expression measures. Bioinformatics (2004) 5.99
A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature (2006) 5.98
Iron-overload-related disease in HFE hereditary hemochromatosis. N Engl J Med (2008) 5.43
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol (2008) 5.38
Exploration, normalization, and genotype calls of high-density oligonucleotide SNP array data. Biostatistics (2006) 5.20
Development of plasmacytoid and conventional dendritic cell subtypes from single precursor cells derived in vitro and in vivo. Nat Immunol (2007) 5.20
Symbiosis insights through metagenomic analysis of a microbial consortium. Nature (2006) 5.04
Summarizing and correcting the GC content bias in high-throughput sequencing. Nucleic Acids Res (2012) 4.94
Glocal alignment: finding rearrangements during alignment. Bioinformatics (2003) 4.88
Strategies and tools for whole-genome alignments. Genome Res (2003) 4.86
Deletion of ultraconserved elements yields viable mice. PLoS Biol (2007) 4.81
The genome of the Western clawed frog Xenopus tropicalis. Science (2010) 4.70
Subtype and pathway specific responses to anticancer compounds in breast cancer. Proc Natl Acad Sci U S A (2011) 4.55
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. Nucleic Acids Res (2004) 4.53
Characterization of evolutionary rates and constraints in three Mammalian genomes. Genome Res (2004) 4.45
Genome-wide experimental determination of barriers to horizontal gene transfer. Science (2007) 4.37
ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet (2010) 4.32
zPicture: dynamic alignment and visualization tool for analyzing conservation profiles. Genome Res (2004) 4.26
Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature (2006) 4.26
Green evolution and dynamic adaptations revealed by genomes of the marine picoeukaryotes Micromonas. Science (2009) 4.05
Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res (2006) 3.92
Cross-species sequence comparisons: a review of methods and available resources. Genome Res (2003) 3.90
Accelerated evolution of conserved noncoding sequences in humans. Science (2006) 3.87
Human-specific gain of function in a developmental enhancer. Science (2008) 3.84
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature (2011) 3.80
Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature (2010) 3.77
The tiny eukaryote Ostreococcus provides genomic insights into the paradox of plankton speciation. Proc Natl Acad Sci U S A (2007) 3.58
Ultraconservation identifies a small subset of extremely constrained developmental enhancers. Nat Genet (2008) 3.55
Genome-wide meta-analysis identifies novel multiple sclerosis susceptibility loci. Ann Neurol (2011) 3.52
Comparative genomics at the vertebrate extremes. Nat Rev Genet (2004) 3.50
Lineage-specific expansion of proteins exported to erythrocytes in malaria parasites. Genome Biol (2006) 3.45
Genomic sequencing of Pleistocene cave bears. Science (2005) 3.40
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci U S A (2012) 3.26
The genome portal of the Department of Energy Joint Genome Institute. Nucleic Acids Res (2011) 3.26
Missense mutations in the sodium-gated potassium channel gene KCNT1 cause severe autosomal dominant nocturnal frontal lobe epilepsy. Nat Genet (2012) 2.98
Spotted long oligonucleotide arrays for human gene expression analysis. Genome Res (2003) 2.95
Evolution and functional classification of vertebrate gene deserts. Genome Res (2004) 2.92
Mulan: multiple-sequence local alignment and visualization for studying function and evolution. Genome Res (2004) 2.91
A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics (2009) 2.90
PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer. Proc Natl Acad Sci U S A (2010) 2.79
Predicting tissue-specific enhancers in the human genome. Genome Res (2007) 2.72
An experimental metagenome data management and analysis system. Bioinformatics (2006) 2.71
Two independent apolipoprotein A5 haplotypes influence human plasma triglyceride levels. Hum Mol Genet (2002) 2.71
Using control genes to correct for unwanted variation in microarray data. Biostatistics (2011) 2.70
Large-scale discovery of enhancers from human heart tissue. Nat Genet (2011) 2.70
Megabase deletions of gene deserts result in viable mice. Nature (2004) 2.68
Functional genomic analysis of oligodendrocyte differentiation. J Neurosci (2006) 2.64
Automated whole-genome multiple alignment of rat, mouse, and human. Genome Res (2004) 2.64
Genomic deletion of a long-range bone enhancer misregulates sclerostin in Van Buchem disease. Genome Res (2005) 2.61
Combinatorial regulation of endothelial gene expression by ets and forkhead transcription factors. Cell (2008) 2.60
MycoCosm portal: gearing up for 1000 fungal genomes. Nucleic Acids Res (2013) 2.60
A regulatory SNP causes a human genetic disease by creating a new transcriptional promoter. Science (2006) 2.58
RegPrecise: a database of curated genomic inferences of transcriptional regulatory interactions in prokaryotes. Nucleic Acids Res (2009) 2.53
The Tasmanian devil transcriptome reveals Schwann cell origins of a clonally transmissible cancer. Science (2010) 2.53
Kufs disease, the major adult form of neuronal ceroid lipofuscinosis, caused by mutations in CLN6. Am J Hum Genet (2011) 2.49