Published in Nature on March 07, 2004
Noise in gene expression: origins, consequences, and control. Science (2005) 9.64
The genome of the social amoeba Dictyostelium discoideum. Nature (2005) 9.18
The chemical genomic portrait of yeast: uncovering a phenotype for all genes. Science (2008) 8.52
The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52
Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol (2005) 6.46
Why highly expressed proteins evolve slowly. Proc Natl Acad Sci U S A (2005) 6.19
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res (2005) 5.87
CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res (2005) 5.25
The genome of the basidiomycetous yeast and human pathogen Cryptococcus neoformans. Science (2005) 4.74
A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell (2008) 4.49
Widespread genome duplications throughout the history of flowering plants. Genome Res (2006) 4.07
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol (2006) 4.03
Unraveling ancient hexaploidy through multiply-aligned angiosperm gene maps. Genome Res (2008) 4.02
Rapid subfunctionalization accompanied by prolonged and substantial neofunctionalization in duplicate gene evolution. Genetics (2005) 3.98
Cell cycle regulation of DNA replication. Annu Rev Genet (2007) 3.80
Aneuploidy: cells losing their balance. Genetics (2008) 3.48
Following tetraploidy in an Arabidopsis ancestor, genes were removed preferentially from one homeolog leaving clusters enriched in dose-sensitive genes. Genome Res (2006) 3.41
Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev (2008) 3.35
Functional specificity among ribosomal proteins regulates gene expression. Cell (2007) 3.22
Sequence composition and genome organization of maize. Proc Natl Acad Sci U S A (2004) 3.22
Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res (2007) 3.12
Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci U S A (2011) 2.97
Symbiosis as an adaptive process and source of phenotypic complexity. Proc Natl Acad Sci U S A (2007) 2.96
Specialized ribosomes: a new frontier in gene regulation and organismal biology. Nat Rev Mol Cell Biol (2012) 2.91
Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol (2004) 2.81
Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res (2005) 2.81
Metabolic functions of duplicate genes in Saccharomyces cerevisiae. Genome Res (2005) 2.68
Resurrecting ancestral alcohol dehydrogenases from yeast. Nat Genet (2005) 2.68
Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol (2009) 2.67
The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol (2010) 2.53
Estimating the tempo and mode of gene family evolution from comparative genomic data. Genome Res (2005) 2.50
Network hubs buffer environmental variation in Saccharomyces cerevisiae. PLoS Biol (2008) 2.47
Molecular basis of evolutionary events that shaped the hardness locus in diploid and polyploid wheat species (Triticum and Aegilops). Plant Cell (2005) 2.40
The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun (2014) 2.36
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc Natl Acad Sci U S A (2004) 2.33
Gene and genome duplications: the impact of dosage-sensitivity on the fate of nuclear genes. Chromosome Res (2009) 2.33
Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome. PLoS Genet (2009) 2.32
Mechanisms of genomic rearrangements and gene expression changes in plant polyploids. Bioessays (2006) 2.28
Yeast evolutionary genomics. Nat Rev Genet (2010) 2.27
Modeling complex genetic interactions in a simple eukaryotic genome: actin displays a rich spectrum of complex haploinsufficiencies. Genes Dev (2006) 2.26
Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication. Proc Natl Acad Sci U S A (2007) 2.24
Computational methods for Gene Orthology inference. Brief Bioinform (2011) 2.16
Genomic analysis of the basal lineage fungus Rhizopus oryzae reveals a whole-genome duplication. PLoS Genet (2009) 2.15
Gene loss and movement in the maize genome. Genome Res (2004) 2.11
Deep functional analysis of synII, a 770-kilobase synthetic yeast chromosome. Science (2017) 2.09
Structure and evolution of protein interaction networks: a statistical model for link dynamics and gene duplications. BMC Evol Biol (2004) 2.01
Uneven chromosome contraction and expansion in the maize genome. Genome Res (2006) 1.96
Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics (2006) 1.96
Comparative genomics of protoploid Saccharomycetaceae. Genome Res (2009) 1.96
Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae. Eukaryot Cell (2005) 1.95
Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A (2009) 1.94
Reprogramming of tRNA modifications controls the oxidative stress response by codon-biased translation of proteins. Nat Commun (2012) 1.93
Independent ancient polyploidy events in the sister families Brassicaceae and Cleomaceae. Plant Cell (2006) 1.92
Functional partitioning of yeast co-expression networks after genome duplication. PLoS Biol (2006) 1.92
Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice. BMC Bioinformatics (2006) 1.91
Rapid evolution of expression and regulatory divergences after yeast gene duplication. Proc Natl Acad Sci U S A (2005) 1.88
RPS25 is essential for translation initiation by the Dicistroviridae and hepatitis C viral IRESs. Genes Dev (2009) 1.87
Buffering of crucial functions by paleologous duplicated genes may contribute cyclicality to angiosperm genome duplication. Proc Natl Acad Sci U S A (2006) 1.87
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) (2011) 1.86
Concern Protein under-wrapping causes dosage sensitivity and decreases gene duplicability. PLoS Genet (2007) 1.80
A genome triplication associated with early diversification of the core eudicots. Genome Biol (2012) 1.80
Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell. Nucleic Acids Res (2005) 1.77
Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution. BMC Biol (2008) 1.77
Increased glycolytic flux as an outcome of whole-genome duplication in yeast. Mol Syst Biol (2007) 1.76
An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Mol Syst Biol (2009) 1.75
Genome-wide fitness test and mechanism-of-action studies of inhibitory compounds in Candida albicans. PLoS Pathog (2007) 1.74
Analysis of genetic systems using experimental evolution and whole-genome sequencing. Genome Biol (2007) 1.72
Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploid cotton (gossypium). Genetics (2009) 1.71
Asynchronous nuclear division cycles in multinucleated cells. J Cell Biol (2006) 1.70
Identification and characterization of upstream open reading frames (uORF) in the 5' untranslated regions (UTR) of genes in Saccharomyces cerevisiae. Curr Genet (2005) 1.70
GIGA: a simple, efficient algorithm for gene tree inference in the genomic age. BMC Bioinformatics (2010) 1.69
Backup without redundancy: genetic interactions reveal the cost of duplicate gene loss. Mol Syst Biol (2007) 1.67
Synaptic scaffold evolution generated components of vertebrate cognitive complexity. Nat Neurosci (2012) 1.67
Pervasive and persistent redundancy among duplicated genes in yeast. PLoS Genet (2008) 1.66
cis-Regulatory and protein evolution in orthologous and duplicate genes. Genome Res (2004) 1.65
The evolution of fungal metabolic pathways. PLoS Genet (2014) 1.64
Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol (2006) 1.64
A general mechanism for network-dosage compensation in gene circuits. Science (2010) 1.59
Conserved functions of yeast genes support the duplication, degeneration and complementation model for gene duplication. Genetics (2005) 1.59
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Genome Res (2007) 1.57
Fungal secretome database: integrated platform for annotation of fungal secretomes. BMC Genomics (2010) 1.55
Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution. Genome Res (2010) 1.55
Correlation between sequence conservation and the genomic context after gene duplication. Nucleic Acids Res (2005) 1.54
Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication. Genome Res (2011) 1.53
alpha AD alpha hybrids of Cryptococcus neoformans: evidence of same-sex mating in nature and hybrid fitness. PLoS Genet (2007) 1.52
i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res (2011) 1.51
Evolution of nonstop, no-go and nonsense-mediated mRNA decay and their termination factor-derived components. BMC Evol Biol (2008) 1.49
A Bayesian approach for fast and accurate gene tree reconstruction. Mol Biol Evol (2010) 1.49
Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. Nucleic Acids Res (2006) 1.49
Concern Subfunctionalization reduces the fitness cost of gene duplication in humans by buffering dosage imbalances. BMC Genomics (2011) 1.49
Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics (2012) 1.49
Fungal cytochrome P450 database. BMC Genomics (2008) 1.48
Physical mapping and microsynteny of Brassica rapa ssp. pekinensis genome corresponding to a 222 kbp gene-rich region of Arabidopsis chromosome 4 and partially duplicated on chromosome 5. Mol Genet Genomics (2005) 1.48
An interactional network of genes involved in chitin synthesis in Saccharomyces cerevisiae. BMC Genet (2005) 1.47
Transcriptional regulation of carbohydrate metabolism in the human pathogen Candida albicans. PLoS Pathog (2009) 1.47
Whole-genome duplication in teleost fishes and its evolutionary consequences. Mol Genet Genomics (2014) 1.47
Novel specificities emerge by stepwise duplication of functional modules. Genome Res (2005) 1.47
Extensive concerted evolution of rice paralogs and the road to regaining independence. Genetics (2007) 1.46
Rapid expansion and functional divergence of subtelomeric gene families in yeasts. Curr Biol (2010) 1.46
The extensive and condition-dependent nature of epistasis among whole-genome duplicates in yeast. Genome Res (2008) 1.44
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
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
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 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
Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72
Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00
A molecular signature of metastasis in primary solid tumors. Nat Genet (2002) 21.36
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
International network of cancer genome projects. Nature (2010) 20.35
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
The mammalian epigenome. Cell (2007) 18.13
Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res (2011) 17.21
Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet (2003) 16.51
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47
Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28
Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
Genetic mapping in human disease. Science (2008) 15.12
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med (2002) 14.01
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet (2001) 13.79
A landscape of driver mutations in melanoma. Cell (2012) 12.61
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell (2012) 11.69
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature (2009) 11.46
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A (2012) 11.23
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol (2012) 10.87
Genetic screens in human cells using the CRISPR-Cas9 system. Science (2013) 10.75
Detecting novel associations in large data sets. Science (2011) 10.60
Quality scores and SNP detection in sequencing-by-synthesis systems. Genome Res (2008) 10.49
Reactive oxygen species have a causal role in multiple forms of insulin resistance. Nature (2006) 10.07
Exome sequencing identifies recurrent SPOP, FOXA1 and MED12 mutations in prostate cancer. Nat Genet (2012) 9.93
Evolution and impact of subclonal mutations in chronic lymphocytic leukemia. Cell (2013) 9.24
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res (2005) 8.69
A high-resolution map of human evolutionary constraint using 29 mammals. Nature (2011) 8.67
Integrative analysis of the melanoma transcriptome. Genome Res (2010) 8.46
Lessons from the cancer genome. Cell (2013) 8.12
A catalog of reference genomes from the human microbiome. Science (2010) 8.10
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
Loss of E-cadherin promotes metastasis via multiple downstream transcriptional pathways. Cancer Res (2008) 7.91
Melanoma genome sequencing reveals frequent PREX2 mutations. Nature (2012) 7.77
Sequence analysis of mutations and translocations across breast cancer subtypes. Nature (2012) 7.76
Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature (2005) 7.74
Integrative genomic approaches identify IKBKE as a breast cancer oncogene. Cell (2007) 7.60
Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications. Nat Biotechnol (2011) 7.53
Highly parallel identification of essential genes in cancer cells. Proc Natl Acad Sci U S A (2008) 7.45
Stochastic state transitions give rise to phenotypic equilibrium in populations of cancer cells. Cell (2011) 7.30
Punctuated evolution of prostate cancer genomes. Cell (2013) 7.23
Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing. Proc Natl Acad Sci U S A (2012) 7.14
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
The genome sequence of the rice blast fungus Magnaporthe grisea. Nature (2005) 6.95
Clonal hematopoiesis and blood-cancer risk inferred from blood DNA sequence. N Engl J Med (2014) 6.89
Identification of a gene causing human cytochrome c oxidase deficiency by integrative genomics. Proc Natl Acad Sci U S A (2003) 6.87
Integrated analysis of protein composition, tissue diversity, and gene regulation in mouse mitochondria. Cell (2003) 6.77
Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol (2006) 6.73
Genetic evidence for complex speciation of humans and chimpanzees. Nature (2006) 6.66
Gene expression signatures define novel oncogenic pathways in T cell acute lymphoblastic leukemia. Cancer Cell (2002) 6.64
The mosaic structure of variation in the laboratory mouse genome. Nature (2002) 6.54
Erralpha and Gabpa/b specify PGC-1alpha-dependent oxidative phosphorylation gene expression that is altered in diabetic muscle. Proc Natl Acad Sci U S A (2004) 6.53
28-way vertebrate alignment and conservation track in the UCSC Genome Browser. Genome Res (2007) 6.42
Core epithelial-to-mesenchymal transition interactome gene-expression signature is associated with claudin-low and metaplastic breast cancer subtypes. Proc Natl Acad Sci U S A (2010) 6.15