The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus.

PubWeight™: 1.86‹?› | Rank: Top 3%

🔗 View Article (PMC 3276118)

Published in G3 (Bethesda) on June 01, 2011

Authors

Devin R Scannell, Oliver A Zill, Antonis Rokas, Celia Payen, Maitreya J Dunham, Michael B Eisen, Jasper Rine, Mark Johnston, Chris Todd Hittinger

Articles citing this

Inferring ancient divergences requires genes with strong phylogenetic signals. Nature (2013) 4.46

A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol (2014) 2.10

Chromosomal rearrangements as a major mechanism in the onset of reproductive isolation in Saccharomyces cerevisiae. Curr Biol (2014) 1.62

Analysis of the Saccharomyces cerevisiae pan-genome reveals a pool of copy number variants distributed in diverse yeast strains from differing industrial environments. Genome Res (2012) 1.39

XRN1 Is a Species-Specific Virus Restriction Factor in Yeasts. PLoS Pathog (2016) 1.38

Ribosome profiling reveals post-transcriptional buffering of divergent gene expression in yeast. Genome Res (2013) 1.35

Putatively noncoding transcripts show extensive association with ribosomes. Genome Biol Evol (2011) 1.28

Evidence for genetic differentiation and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus. Mol Ecol (2011) 1.24

Nonparadoxical evolutionary stability of the recombination initiation landscape in yeast. Science (2015) 1.22

Evolution at two levels of gene expression in yeast. Genome Res (2013) 1.16

Speciation driven by hybridization and chromosomal plasticity in a wild yeast. Nat Microbiol (2016) 1.14

Evolutionary role of interspecies hybridization and genetic exchanges in yeasts. Microbiol Mol Biol Rev (2012) 1.11

A Gondwanan imprint on global diversity and domestication of wine and cider yeast Saccharomyces uvarum. Nat Commun (2014) 1.09

The Genome Sequence of Saccharomyces eubayanus and the Domestication of Lager-Brewing Yeasts. Mol Biol Evol (2015) 1.06

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data. PLoS One (2013) 1.04

High quality de novo sequencing and assembly of the Saccharomyces arboricolus genome. BMC Genomics (2013) 1.03

Negative feedback confers mutational robustness in yeast transcription factor regulation. Proc Natl Acad Sci U S A (2012) 1.01

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms. Elife (2014) 1.01

Deciphering the hybridisation history leading to the Lager lineage based on the mosaic genomes of Saccharomyces bayanus strains NBRC1948 and CBS380. PLoS One (2011) 1.00

Selection on noise constrains variation in a eukaryotic promoter. Nature (2015) 0.99

APJ1 and GRE3 homologs work in concert to allow growth in xylose in a natural Saccharomyces sensu stricto hybrid yeast. Genetics (2012) 0.93

Characterization of chromosome stability in diploid, polyploid and hybrid yeast cells. PLoS One (2013) 0.91

Evaluating Phylostratigraphic Evidence for Widespread De Novo Gene Birth in Genome Evolution. Mol Biol Evol (2016) 0.91

Evidence for the robustness of protein complexes to inter-species hybridization. PLoS Genet (2012) 0.90

The complex evolutionary dynamics of Hsp70s: a genomic and functional perspective. Genome Biol Evol (2013) 0.90

Centromere-like regions in the budding yeast genome. PLoS Genet (2013) 0.90

Whole Genome Comparison Reveals High Levels of Inbreeding and Strain Redundancy Across the Spectrum of Commercial Wine Strains of Saccharomyces cerevisiae. G3 (Bethesda) (2016) 0.89

Introducing a new breed of wine yeast: interspecific hybridisation between a commercial Saccharomyces cerevisiae wine yeast and Saccharomyces mikatae. PLoS One (2013) 0.88

Enhanced enzymatic activity of glycerol-3-phosphate dehydrogenase from the cryophilic Saccharomyces kudriavzevii. PLoS One (2014) 0.88

Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Sci Rep (2015) 0.86

Coupling unbiased mutagenesis to high-throughput DNA sequencing uncovers functional domains in the Ndc80 kinetochore protein of Saccharomyces cerevisiae. Genetics (2013) 0.84

Inferring evolutionary histories of pathway regulation from transcriptional profiling data. PLoS Comput Biol (2013) 0.84

Genomics and the making of yeast biodiversity. Curr Opin Genet Dev (2015) 0.83

Evolution of a membrane protein regulon in Saccharomyces. Mol Biol Evol (2012) 0.83

Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus. Genome Res (2016) 0.83

Loss of heterozygosity drives adaptation in hybrid yeast. Mol Biol Evol (2017) 0.83

Genomic insights into the Saccharomyces sensu stricto complex. Genetics (2015) 0.82

Accurate identification of centromere locations in yeast genomes using Hi-C. Nucleic Acids Res (2015) 0.82

Comparative gene expression between two yeast species. BMC Genomics (2013) 0.82

Biogeographical characterization of Saccharomyces cerevisiae wine yeast by molecular methods. Front Microbiol (2013) 0.82

Characterization and prediction of haploinsufficiency using systems-level gene properties in yeast. G3 (Bethesda) (2013) 0.81

The adjacent positioning of co-regulated gene pairs is widely conserved across eukaryotes. BMC Genomics (2012) 0.81

A new system for comparative functional genomics of Saccharomyces yeasts. Genetics (2013) 0.81

Evidence of Natural Hybridization in Brazilian Wild Lineages of Saccharomyces cerevisiae. Genome Biol Evol (2016) 0.80

Universal distribution of mutational effects on protein stability, uncoupling of protein robustness from sequence evolution and distinct evolutionary modes of prokaryotic and eukaryotic proteins. Phys Biol (2015) 0.79

Post-zygotic sterility and cytonuclear compatibility limits in S. cerevisiae xenomitochondrial cybrids. Front Genet (2015) 0.79

Reconstruction of the evolutionary history of Saccharomyces cerevisiae x S. kudriavzevii hybrids based on multilocus sequence analysis. PLoS One (2012) 0.79

High-efficiency genome editing and allele replacement in prototrophic and wild strains of Saccharomyces. Genetics (2014) 0.79

Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data. G3 (Bethesda) (2016) 0.78

Genome Sequence and Analysis of a Stress-Tolerant, Wild-Derived Strain of Saccharomyces cerevisiae Used in Biofuels Research. G3 (Bethesda) (2016) 0.78

Lipids containing medium-chain fatty acids are specific to post-whole genome duplication Saccharomycotina yeasts. BMC Evol Biol (2015) 0.78

Efficient engineering of marker-free synthetic allotetraploids of Saccharomyces. Fungal Genet Biol (2015) 0.78

Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software. BMC Genomics (2014) 0.78

Genome Sequencing and Comparative Analysis of Saccharomyces cerevisiae Strains of the Peterhof Genetic Collection. PLoS One (2016) 0.77

Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters. Genome Res (2014) 0.77

Global mapping of DNA conformational flexibility on Saccharomyces cerevisiae. PLoS Comput Biol (2015) 0.77

Characterisation of the broad substrate specificity 2-keto acid decarboxylase Aro10p of Saccharomyces kudriavzevii and its implication in aroma development. Microb Cell Fact (2016) 0.77

Ploidy influences the functional attributes of de novo lager yeast hybrids. Appl Microbiol Biotechnol (2016) 0.77

Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production. Biotechnol Biofuels (2017) 0.76

Polygenic evolution of a sugar specialization trade-off in yeast. Nature (2016) 0.76

Role of mRNA structure in the control of protein folding. Nucleic Acids Res (2016) 0.76

Ongoing resolution of duplicate gene functions shapes the diversification of a metabolic network. Elife (2016) 0.75

The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast. Genome Biol Evol (2016) 0.75

Differences in environmental stress response among yeasts is consistent with species-specific lifestyles. Mol Biol Cell (2016) 0.75

Evolutionary analysis of heterochromatin protein compatibility by interspecies complementation in Saccharomyces. Genetics (2012) 0.75

Major sulfonate transporter Soa1 in Saccharomyces cerevisiae and considerable substrate diversity in its fungal family. Nat Commun (2017) 0.75

Iron-Sulfur Cluster Biogenesis Chaperones: Evidence for Emergence of Mutational Robustness of a Highly Specific Protein-Protein Interaction. Mol Biol Evol (2015) 0.75

Evolution of protein-protein interaction networks in yeast. PLoS One (2017) 0.75

Differential paralog divergence modulates genome evolution across yeast species. PLoS Genet (2017) 0.75

Dissecting the Genetic Basis of a Complex cis-Regulatory Adaptation. PLoS Genet (2015) 0.75

2μ plasmid in Saccharomyces species and in Saccharomyces cerevisiae. FEMS Yeast Res (2015) 0.75

Known mutator alleles do not markedly increase mutation rate in clinical Saccharomyces cerevisiae strains. Proc Biol Sci (2017) 0.75

European derived Saccharomyces cerevisiae colonisation of New Zealand vineyards aided by humans. FEMS Yeast Res (2016) 0.75

Effect of Temperature on the Prevalence of Saccharomyces Non cerevisiae Species against a S. cerevisiae Wine Strain in Wine Fermentation: Competition, Physiological Fitness, and Influence in Final Wine Composition. Front Microbiol (2017) 0.75

Pathway swapping: Toward modular engineering of essential cellular processes. Proc Natl Acad Sci U S A (2016) 0.75

Taxonomically Restricted Genes with Essential Functions Frequently Play Roles in Chromosome Segregation in Caenorhabditis elegans and Saccharomyces cerevisiae. G3 (Bethesda) (2017) 0.75

Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species. Genome Biol Evol (2017) 0.75

Mitochondrial genome evolution in the Saccharomyces sensu stricto complex. PLoS One (2017) 0.75

Evolutionary biology through the lens of budding yeast comparative genomics. Nat Rev Genet (2017) 0.75

Articles cited by this

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31

Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res (2008) 151.16

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res (1997) 142.55

Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res (1998) 106.16

BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13

Additional modules for versatile and economical PCR-based gene deletion and modification in Saccharomyces cerevisiae. Yeast (1998) 48.29

De novo assembly of human genomes with massively parallel short read sequencing. Genome Res (2009) 45.91

PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68

Life with 6000 genes. Science (1996) 41.51

Relaxed phylogenetics and dating with confidence. PLoS Biol (2006) 37.68

Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16

Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics (2005) 24.54

The evolutionary fate and consequences of duplicate genes. Science (2000) 24.22

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science (2003) 16.49

The genome sequence of Schizosaccharomyces pombe. Nature (2002) 14.26

Three new dominant drug resistance cassettes for gene disruption in Saccharomyces cerevisiae. Yeast (1999) 14.19

Molecular evidence for an ancient duplication of the entire yeast genome. Nature (1997) 13.86

The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol (2003) 13.32

Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature (2004) 12.32

Population genomics of domestic and wild yeasts. Nature (2009) 11.79

A new efficient gene disruption cassette for repeated use in budding yeast. Nucleic Acids Res (1996) 11.05

Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature (2003) 10.73

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines. Nature (2010) 10.66

Genome evolution in yeasts. Nature (2004) 10.50

DNA sequence quality trimming and vector removal. Bioinformatics (2001) 10.04

A new generation of homology search tools based on probabilistic inference. Genome Inform (2009) 8.93

Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences. Mol Biol Evol (2005) 8.42

Natural history and evolutionary principles of gene duplication in fungi. Nature (2007) 7.26

The Ashbya gossypii genome as a tool for mapping the ancient Saccharomyces cerevisiae genome. Science (2004) 6.25

Fast statistical alignment. PLoS Comput Biol (2009) 5.92

Evolution of pathogenicity and sexual reproduction in eight Candida genomes. Nature (2009) 5.90

The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species. Genome Res (2005) 5.87

RevTrans: Multiple alignment of coding DNA from aligned amino acid sequences. Nucleic Acids Res (2003) 4.45

Saccharomyces cerevisiae S288C has a mutation in FLO8, a gene required for filamentous growth. Genetics (1996) 4.39

In vivo site-directed mutagenesis using oligonucleotides. Nat Biotechnol (2001) 3.65

The chromosome ends of Saccharomyces cerevisiae. Yeast (1995) 3.60

Emerging principles of regulatory evolution. Proc Natl Acad Sci U S A (2007) 3.42

Multiple rounds of speciation associated with reciprocal gene loss in polyploid yeasts. Nature (2006) 3.39

Saccharomyces Genome Database provides mutant phenotype data. Nucleic Acids Res (2009) 3.38

Phylogenetic relationships among yeasts of the 'Saccharomyces complex' determined from multigene sequence analyses. FEMS Yeast Res (2003) 3.34

RNAi in budding yeast. Science (2009) 3.32

A yeast hybrid provides insight into the evolution of gene expression regulation. Science (2009) 3.25

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing. BMC Genomics (2009) 3.22

Incompatibility of nuclear and mitochondrial genomes causes hybrid sterility between two yeast species. Cell (2008) 2.94

Widespread genetic incompatibility in C. elegans maintained by balancing selection. Science (2008) 2.84

The delitto perfetto approach to in vivo site-directed mutagenesis and chromosome rearrangements with synthetic oligonucleotides in yeast. Methods Enzymol (2006) 2.84

Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol (2004) 2.81

Figaro: a novel statistical method for vector sequence removal. Bioinformatics (2008) 2.81

Dating divergences in the Fungal Tree of Life: review and new analyses. Mycologia (2007) 2.75

Sequence diversity, reproductive isolation and species concepts in Saccharomyces. Genetics (2006) 2.70

Genetic interactions between transcription factors cause natural variation in yeast. Science (2009) 2.62

Chromosomal evolution in Saccharomyces. Nature (2000) 2.53

Automatic genome-wide reconstruction of phylogenetic gene trees. Bioinformatics (2007) 2.52

Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc Natl Acad Sci U S A (2004) 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

Fitness and its role in evolutionary genetics. Nat Rev Genet (2009) 2.29

Yeast evolutionary genomics. Nat Rev Genet (2010) 2.27

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

Three new species in the Saccharomyces sensu stricto complex: Saccharomyces cariocanus, Saccharomyces kudriavzevii and Saccharomyces mikatae. Int J Syst Evol Microbiol (2000) 2.23

Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature (2010) 2.18

Variations in stress sensitivity and genomic expression in diverse S. cerevisiae isolates. PLoS Genet (2008) 2.08

Yeasts illustrate the molecular mechanisms of eukaryotic genome evolution. Trends Genet (2006) 2.06

Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics (2006) 1.96

Comparative genomics of protoploid Saccharomycetaceae. Genome Res (2009) 1.96

Natural populations of Saccharomyces kudriavzevii in Portugal are associated with oak bark and are sympatric with S. cerevisiae and S. paradoxus. Appl Environ Microbiol (2008) 1.94

Multiple molecular mechanisms cause reproductive isolation between three yeast species. PLoS Biol (2010) 1.87

A 'natural' mutation in Saccharomyces cerevisiae strains derived from S288c affects the complex regulatory gene HAP1 (CYP1). Curr Genet (1999) 1.80

Polygenic and directional regulatory evolution across pathways in Saccharomyces. Proc Natl Acad Sci U S A (2010) 1.75

The reacquisition of biotin prototrophy in Saccharomyces cerevisiae involved horizontal gene transfer, gene duplication and gene clustering. Genetics (2007) 1.69

Systematic planning of genome-scale experiments in poorly studied species. PLoS Comput Biol (2010) 1.66

Yeast genome evolution--the origin of the species. Yeast (2007) 1.60

Predicting cellular growth from gene expression signatures. PLoS Comput Biol (2009) 1.50

New hybrids between Saccharomyces sensu stricto yeast species found among wine and cider production strains. Appl Environ Microbiol (1998) 1.49

Hybrid speciation in experimental populations of yeast. Science (2002) 1.49

Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. Nucleic Acids Res (2006) 1.49

Genome sequence of the lager brewing yeast, an interspecies hybrid. DNA Res (2009) 1.44

A burst of protein sequence evolution and a prolonged period of asymmetric evolution follow gene duplication in yeast. Genome Res (2007) 1.43

Reproductive isolation in Saccharomyces. Heredity (Edinb) (2008) 1.42

After the duplication: gene loss and adaptation in Saccharomyces genomes. Genetics (2005) 1.40

Adaptive evolution by mutations in the FLO11 gene. Proc Natl Acad Sci U S A (2006) 1.38

Yeast genome sequencing: the power of comparative genomics. Mol Microbiol (2004) 1.36

A role for the mismatch repair system during incipient speciation in Saccharomyces. J Evol Biol (2003) 1.33

Incipient balancing selection through adaptive loss of aquaporins in natural Saccharomyces cerevisiae populations. PLoS Genet (2010) 1.21

Interspecies variation reveals a conserved repressor of alpha-specific genes in Saccharomyces yeasts. Genes Dev (2008) 1.18

Molecular characterization of new natural hybrids of Saccharomyces cerevisiae and S. kudriavzevii in brewing. Appl Environ Microbiol (2008) 1.16

Speciation through cytonuclear incompatibility: insights from yeast and implications for higher eukaryotes. Bioessays (2010) 1.14

Hypervariable noncoding sequences in Saccharomyces cerevisiae. Genetics (2005) 1.12

Saccharomyces arboricolus sp. nov., a yeast species from tree bark. Int J Syst Evol Microbiol (2008) 1.10

Fishing for the secrets of vertebrate evolution in threespine sticklebacks. Dev Dyn (2005) 1.08

Co-evolution of transcriptional silencing proteins and the DNA elements specifying their assembly. PLoS Biol (2010) 1.07

Generation of a large set of genetically tractable haploid and diploid Saccharomyces strains. FEMS Yeast Res (2009) 1.06

What can comparative genomics tell us about species concepts in the genus Aspergillus? Stud Mycol (2007) 0.96

From sequence to function: Insights from natural variation in budding yeasts. Biochim Biophys Acta (2011) 0.92

Telomere behavior in a hybrid yeast. Cell Res (2009) 0.85

Elaboration, diversification and regulation of the Sir1 family of silencing proteins in Saccharomyces. Genetics (2009) 0.85

Articles by these authors

Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10

Global mapping of the yeast genetic interaction network. Science (2004) 21.34

Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01

Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science (2003) 16.49

Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures. Nature (2007) 11.66

In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60

Exploiting transcription factor binding site clustering to identify cis-regulatory modules involved in pattern formation in the Drosophila genome. Proc Natl Acad Sci U S A (2002) 8.56

Effects of aneuploidy on cellular physiology and cell division in haploid yeast. Science (2007) 7.69

The Paf1 complex is required for histone H3 methylation by COMPASS and Dot1p: linking transcriptional elongation to histone methylation. Mol Cell (2003) 7.47

The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Annu Rev Biochem (2003) 7.22

The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature (2008) 6.69

Tools for neuroanatomy and neurogenetics in Drosophila. Proc Natl Acad Sci U S A (2008) 6.35

Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol (2008) 6.30

A quantitative spatiotemporal atlas of gene expression in the Drosophila blastoderm. Cell (2008) 5.63

Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol (2009) 5.23

A protein complex containing the conserved Swi2/Snf2-related ATPase Swr1p deposits histone variant H2A.Z into euchromatin. PLoS Biol (2004) 5.02

The Paleozoic origin of enzymatic lignin decomposition reconstructed from 31 fungal genomes. Science (2012) 4.93

Methylation of histone H3 by COMPASS requires ubiquitination of histone H2B by Rad6. J Biol Chem (2002) 4.75

Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter. Mol Cell (2003) 4.49

Inferring ancient divergences requires genes with strong phylogenetic signals. Nature (2013) 4.46

Serendipitous discovery of Wolbachia genomes in multiple Drosophila species. Genome Biol (2005) 4.42

Noise minimization in eukaryotic gene expression. PLoS Biol (2004) 4.36

Exploring the conditional coregulation of yeast gene expression through fuzzy k-means clustering. Genome Biol (2002) 4.24

Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature (2006) 4.21

COMPASS, a histone H3 (Lysine 4) methyltransferase required for telomeric silencing of gene expression. J Biol Chem (2002) 4.05

Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol (2006) 4.01

Benchmarking tools for the alignment of functional noncoding DNA. BMC Bioinformatics (2004) 4.00

The Paf1 complex is essential for histone monoubiquitination by the Rad6-Bre1 complex, which signals for histone methylation by COMPASS and Dot1p. J Biol Chem (2003) 3.81

Identification of aneuploidy-tolerating mutations. Cell (2010) 3.73

The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet (2008) 3.58

Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci U S A (2008) 3.45

Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura. Genome Biol (2004) 3.36

Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science (2006) 3.32

Three-dimensional morphology and gene expression in the Drosophila blastoderm at cellular resolution I: data acquisition pipeline. Genome Biol (2006) 3.22

MONKEY: identifying conserved transcription-factor binding sites in multiple alignments using a binding site-specific evolutionary model. Genome Biol (2004) 3.15

Why PLoS became a publisher. PLoS Biol (2003) 3.09

Dysplasia and cancer in a large multicenter cohort of patients with Barrett's esophagus. Clin Gastroenterol Hepatol (2006) 3.06

Functional genomic analysis of the rates of protein evolution. Proc Natl Acad Sci U S A (2005) 3.04

Widespread discordance of gene trees with species tree in Drosophila: evidence for incomplete lineage sorting. PLoS Genet (2006) 3.01

Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation. Mol Cell (2009) 2.91

Conservation and evolution of cis-regulatory systems in ascomycete fungi. PLoS Biol (2004) 2.81

Bayesian estimation of concordance among gene trees. Mol Biol Evol (2006) 2.81

Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol Biol Cell (2002) 2.80

Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res (2006) 2.75

Association of cohesin and Nipped-B with transcriptionally active regions of the Drosophila melanogaster genome. Chromosoma (2007) 2.73

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding. Genome Biol (2011) 2.68

Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet (2008) 2.67

Position specific variation in the rate of evolution in transcription factor binding sites. BMC Evol Biol (2003) 2.67

Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development. PLoS Genet (2011) 2.65

Impact of chromatin structures on DNA processing for genomic analyses. PLoS One (2009) 2.63

Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol (2011) 2.43

Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc Natl Acad Sci U S A (2004) 2.33

Highly expressed loci are vulnerable to misleading ChIP localization of multiple unrelated proteins. Proc Natl Acad Sci U S A (2013) 2.33

Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol (2010) 2.32

Benchmarking next-generation transcriptome sequencing for functional and evolutionary genomics. Mol Biol Evol (2009) 2.32

Comparing whole genomes using DNA microarrays. Nat Rev Genet (2008) 2.27

Transcriptome profiling of chemosensory appendages in the malaria vector Anopheles gambiae reveals tissue- and sex-specific signatures of odor coding. BMC Genomics (2011) 2.22

Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature (2010) 2.18

Glucose sensing and signaling in Saccharomyces cerevisiae through the Rgt2 glucose sensor and casein kinase I. Proc Natl Acad Sci U S A (2004) 2.10

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast. Proc Natl Acad Sci U S A (2011) 2.04

Telomeric heterochromatin boundaries require NuA4-dependent acetylation of histone variant H2A.Z in Saccharomyces cerevisiae. Genes Dev (2006) 2.01

Control of embryonic stem cell lineage commitment by core promoter factor, TAF3. Cell (2011) 2.00

The Bur1/Bur2 complex is required for histone H2B monoubiquitination by Rad6/Bre1 and histone methylation by COMPASS. Mol Cell (2005) 1.99

Regulatory network connecting two glucose signal transduction pathways in Saccharomyces cerevisiae. Eukaryot Cell (2004) 1.99

Coevolution of gene expression among interacting proteins. Proc Natl Acad Sci U S A (2004) 1.96

Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae. Genome Biol (2004) 1.96

Functional analysis of gene duplications in Saccharomyces cerevisiae. Genetics (2006) 1.96

Comparative genomics of protoploid Saccharomycetaceae. Genome Res (2009) 1.96

Zelda binding in the early Drosophila melanogaster embryo marks regions subsequently activated at the maternal-to-zygotic transition. PLoS Genet (2011) 1.95

Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila evolution. Cell (2006) 1.92

Evolutionary mirages: selection on binding site composition creates the illusion of conserved grammars in Drosophila enhancers. PLoS Genet (2010) 1.92

Accurate detection of aneuploidies in array CGH and gene expression microarray data. Bioinformatics (2004) 1.89

Yeast genome duplication was followed by asynchronous differentiation of duplicated genes. Nature (2003) 1.84

New roles for model genetic organisms in understanding and treating human disease: report from the 2006 Genetics Society of America meeting. Genetics (2006) 1.83

Mapping novel traits by array-assisted bulk segregant analysis in Saccharomyces cerevisiae. Genetics (2006) 1.81

Identification of regulatory elements using a feature selection method. Bioinformatics (2002) 1.80

Recurrent tissue-specific mtDNA mutations are common in humans. PLoS Genet (2013) 1.77

Specificity and regulation of DNA binding by the yeast glucose transporter gene repressor Rgt1. Mol Cell Biol (2003) 1.77

Aging and gene expression in the primate brain. PLoS Biol (2005) 1.76

Genome-wide consequences of deleting any single gene. Mol Cell (2013) 1.76

Transcriptional consequences of aneuploidy. Proc Natl Acad Sci U S A (2012) 1.70

The relation of body mass index to depressive symptoms. Can J Public Health (2004) 1.67

A role for yeast oxysterol-binding protein homologs in endocytosis and in the maintenance of intracellular sterol-lipid distribution. J Cell Sci (2004) 1.67

GATA: a graphic alignment tool for comparative sequence analysis. BMC Bioinformatics (2005) 1.66

Slx4 regulates DNA damage checkpoint-dependent phosphorylation of the BRCT domain protein Rtt107/Esc4. Mol Biol Cell (2005) 1.66

Identification of oligonucleotide sequences that direct the movement of the Escherichia coli FtsK translocase. Proc Natl Acad Sci U S A (2005) 1.66

A condensin-like dosage compensation complex acts at a distance to control expression throughout the genome. Genes Dev (2009) 1.64

The Drosophila melanogaster sir2+ gene is nonessential and has only minor effects on position-effect variegation. Genetics (2003) 1.63

Non-optimal codon usage is a mechanism to achieve circadian clock conditionality. Nature (2013) 1.61

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life. Proc Natl Acad Sci U S A (2010) 1.55

Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A/B family members. Mol Cell (2009) 1.52

Comparing bootstrap and posterior probability values in the four-taxon case. Syst Biol (2003) 1.50

Predicting cellular growth from gene expression signatures. PLoS Comput Biol (2009) 1.50