Genome evolution in yeasts.

The genome of the social amoeba Dictyostelium discoideum. Nature (2005) 9.18

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

CYGD: the Comprehensive Yeast Genome Database. Nucleic Acids Res (2005) 5.25

InParanoid 6: eukaryotic ortholog clusters with inparalogs. Nucleic Acids Res (2007) 4.15

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol (2006) 4.03

Comprehensive polymorphism survey elucidates population structure of Saccharomyces cerevisiae. Nature (2009) 3.67

The evolution of combinatorial gene regulation in fungi. PLoS Biol (2008) 3.53

Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev (2008) 3.35

Candida albicans and Candida glabrata clinical isolates exhibiting reduced echinocandin susceptibility. Antimicrob Agents Chemother (2006) 3.19

An ancestral oomycete locus contains late blight avirulence gene Avr3a, encoding a protein that is recognized in the host cytoplasm. Proc Natl Acad Sci U S A (2005) 3.06

A human-curated annotation of the Candida albicans genome. PLoS Genet (2005) 3.04

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res (2012) 3.02

Phylogenetic and structural analysis of centromeric DNA and kinetochore proteins. Genome Biol (2006) 2.99

A phenotypic profile of the Candida albicans regulatory network. PLoS Genet (2009) 2.86

Mapping of transcription start sites in Saccharomyces cerevisiae using 5' SAGE. Nucleic Acids Res (2005) 2.81

Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species. PLoS Biol (2009) 2.67

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118. Proc Natl Acad Sci U S A (2009) 2.51

Efflux-mediated antifungal drug resistance. Clin Microbiol Rev (2009) 2.44

The genome sequence of the model ascomycete fungus Podospora anserina. Genome Biol (2008) 2.43

Gene gain and loss during evolution of obligate parasitism in the white rust pathogen of Arabidopsis thaliana. PLoS Biol (2011) 2.38

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

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

The Candida genome database incorporates multiple Candida species: multispecies search and analysis tools with curated gene and protein information for Candida albicans and Candida glabrata. Nucleic Acids Res (2011) 2.18

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

Systematic phenotyping of a large-scale Candida glabrata deletion collection reveals novel antifungal tolerance genes. PLoS Pathog (2014) 1.98

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

Adaptive evolution of centromere proteins in plants and animals. J Biol (2004) 1.90

The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) (2011) 1.86

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

Candida glabrata PDR1, a transcriptional regulator of a pleiotropic drug resistance network, mediates azole resistance in clinical isolates and petite mutants. Antimicrob Agents Chemother (2006) 1.70

Formation of new chromosomes as a virulence mechanism in yeast Candida glabrata. Proc Natl Acad Sci U S A (2009) 1.69

Comparative genome analysis of filamentous fungi reveals gene family expansions associated with fungal pathogenesis. PLoS One (2008) 1.68

Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol (2010) 1.67

Browsing repeats in genomes: Pygram and an application to non-coding region analysis. BMC Bioinformatics (2006) 1.65

A phylogenomic profile of globins. BMC Evol Biol (2006) 1.64

Specificity and evolvability in eukaryotic protein interaction networks. PLoS Comput Biol (2006) 1.64

Genome, secretome and glucose transport highlight unique features of the protein production host Pichia pastoris. Microb Cell Fact (2009) 1.63

Debaryomyces hansenii (Candida famata), a rare human fungal pathogen often misidentified as Pichia guilliermondii (Candida guilliermondii). J Clin Microbiol (2008) 1.57

Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes. Genome Res (2007) 1.57

Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res (2005) 1.56

Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. Nucleic Acids Res (2008) 1.56

Fungal secretome database: integrated platform for annotation of fungal secretomes. BMC Genomics (2010) 1.55

Phylogeny-wide analysis of social amoeba genomes highlights ancient origins for complex intercellular communication. Genome Res (2011) 1.53

i-ADHoRe 3.0--fast and sensitive detection of genomic homology in extremely large data sets. Nucleic Acids Res (2011) 1.51

MYBS: a comprehensive web server for mining transcription factor binding sites in yeast. Nucleic Acids Res (2007) 1.50

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

Fungal cytochrome P450 database. BMC Genomics (2008) 1.48

Transport of magnesium and other divalent cations: evolution of the 2-TM-GxN proteins in the MIT superfamily. Mol Genet Genomics (2005) 1.47

Novel specificities emerge by stepwise duplication of functional modules. Genome Res (2005) 1.47

An evolutionary and functional assessment of regulatory network motifs. Genome Biol (2005) 1.45

Genome characterization of the oleaginous fungus Mortierella alpina. PLoS One (2011) 1.43

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

VGSC: A Web-Based Vector Graph Toolkit of Genome Synteny and Collinearity. Biomed Res Int (2016) 1.43

A molecular genetic toolbox for Yarrowia lipolytica. Biotechnol Biofuels (2017) 1.41

Phylogenetic diversity of stress signalling pathways in fungi. BMC Evol Biol (2009) 1.40

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

Highly variable rates of genome rearrangements between hemiascomycetous yeast lineages. PLoS Genet (2006) 1.40

Comparative genomics of xylose-fermenting fungi for enhanced biofuel production. Proc Natl Acad Sci U S A (2011) 1.39

CFGP: a web-based, comparative fungal genomics platform. Nucleic Acids Res (2007) 1.39

Specificity in protein interactions and its relationship with sequence diversity and coevolution. Proc Natl Acad Sci U S A (2007) 1.39

Polymorphisms in multiple genes contribute to the spontaneous mitochondrial genome instability of Saccharomyces cerevisiae S288C strains. Genetics (2009) 1.38

Production of omega-3 eicosapentaenoic acid by metabolic engineering of Yarrowia lipolytica. Nat Biotechnol (2013) 1.38

Evaluating ortholog prediction algorithms in a yeast model clade. PLoS One (2011) 1.37

Candida glabrata: a review of its features and resistance. Eur J Clin Microbiol Infect Dis (2013) 1.36

Moonlighting proteins in yeasts. Microbiol Mol Biol Rev (2008) 1.36

Improvement of xylose uptake and ethanol production in recombinant Saccharomyces cerevisiae through an inverse metabolic engineering approach. Appl Environ Microbiol (2005) 1.36

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. Database (Oxford) (2014) 1.36

Measuring the evolutionary rewiring of biological networks. PLoS Comput Biol (2011) 1.35

Characterization of three classes of membrane proteins involved in fungal azole resistance by functional hyperexpression in Saccharomyces cerevisiae. Eukaryot Cell (2007) 1.35

Consistent patterns of rate asymmetry and gene loss indicate widespread neofunctionalization of yeast genes after whole-genome duplication. Genetics (2006) 1.34

Gene duplication and the evolution of ribosomal protein gene regulation in yeast. Proc Natl Acad Sci U S A (2010) 1.33

Candida albicans hyphal formation and virulence assessed using a Caenorhabditis elegans infection model. Eukaryot Cell (2009) 1.33

Operons. Cell Mol Life Sci (2009) 1.33

Analysis of gene evolution and metabolic pathways using the Candida Gene Order Browser. BMC Genomics (2010) 1.33

Trs85 is required for macroautophagy, pexophagy and cytoplasm to vacuole targeting in Yarrowia lipolytica and Saccharomyces cerevisiae. Autophagy (2005) 1.32

Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl Environ Microbiol (2011) 1.31

Adaptive laboratory evolution -- principles and applications for biotechnology. Microb Cell Fact (2013) 1.29

Proteins with two SUMO-like domains in chromatin-associated complexes: the RENi (Rad60-Esc2-NIP45) family. BMC Bioinformatics (2005) 1.29

Epigenetically-inherited centromere and neocentromere DNA replicates earliest in S-phase. PLoS Genet (2010) 1.29

Yapsins are a family of aspartyl proteases required for cell wall integrity in Saccharomyces cerevisiae. Eukaryot Cell (2005) 1.29

Genolevures complete genomes provide data and tools for comparative genomics of hemiascomycetous yeasts. Nucleic Acids Res (2006) 1.28

Comparative genome analysis across a kingdom of eukaryotic organisms: specialization and diversification in the fungi. Genome Res (2007) 1.28

The RNA polymerase III-dependent family of genes in hemiascomycetes: comparative RNomics, decoding strategies, transcription and evolutionary implications. Nucleic Acids Res (2006) 1.28

Sequence and comparative genomic analysis of actin-related proteins. Mol Biol Cell (2005) 1.28

Evolution of the holozoan ribosome biogenesis regulon. BMC Genomics (2008) 1.25

Promoter-dependent disruption of genes: simple, rapid, and specific PCR-based method with application to three different yeast. Curr Genet (2005) 1.25

Human tRNA genes function as chromatin insulators. EMBO J (2011) 1.25

The evolution of novel fungal genes from non-retroviral RNA viruses. BMC Biol (2009) 1.24

High-temperature ethanol fermentation and transformation with linear DNA in the thermotolerant yeast Kluyveromyces marxianus DMKU3-1042. Appl Environ Microbiol (2008) 1.24

Extensive DNA-binding specificity divergence of a conserved transcription regulator. Proc Natl Acad Sci U S A (2011) 1.24

Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. PLoS Genet (2010) 1.24

Evolutionary erosion of yeast sex chromosomes by mating-type switching accidents. Proc Natl Acad Sci U S A (2011) 1.23

FUNYBASE: a FUNgal phYlogenomic dataBASE. BMC Bioinformatics (2008) 1.22

Loss of mitochondrial functions associated with azole resistance in Candida glabrata results in enhanced virulence in mice. Antimicrob Agents Chemother (2011) 1.21

Parallel evolution of the make-accumulate-consume strategy in Saccharomyces and Dekkera yeasts. Nat Commun (2011) 1.21

A human gut microbial gene catalogue established by metagenomic sequencing. Nature (2010) 43.63

Enterotypes of the human gut microbiome. Nature (2011) 24.36

The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36

The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature (2007) 18.04

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol (2004) 16.08

IntAct: an open source molecular interaction database. Nucleic Acids Res (2004) 15.02

MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res (2006) 12.48

Mutations in PCSK9 cause autosomal dominant hypercholesterolemia. Nat Genet (2003) 11.67

Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med (2006) 11.14

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03

Comparative genome and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science (2002) 9.43

Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature (2005) 8.55

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet (2009) 8.51

Resistance of Plasmodium falciparum field isolates to in-vitro artemether and point mutations of the SERCA-type PfATPase6. Lancet (2005) 8.30

Single processing center models for human Dicer and bacterial RNase III. Cell (2004) 8.19

Broadening the horizon--level 2.5 of the HUPO-PSI format for molecular interactions. BMC Biol (2007) 8.03

Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature (2005) 7.74

Annotating genomes with massive-scale RNA sequencing. Genome Biol (2008) 7.73

Comparison of two neoadjuvant chemoradiotherapy regimens for locally advanced rectal cancer: results of the phase III trial ACCORD 12/0405-Prodige 2. J Clin Oncol (2010) 7.29

Halogen bonds in biological molecules. Proc Natl Acad Sci U S A (2004) 7.19

The Phaeodactylum genome reveals the evolutionary history of diatom genomes. Nature (2008) 6.70

Comparative genomics of multidrug resistance in Acinetobacter baumannii. PLoS Genet (2006) 6.32

The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat Biotechnol (2003) 6.11

Phylogenomics revives traditional views on deep animal relationships. Curr Biol (2009) 5.89

The non-Watson-Crick base pairs and their associated isostericity matrices. Nucleic Acids Res (2002) 5.35

RNAML: a standard syntax for exchanging RNA information. RNA (2002) 5.34

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol (2008) 5.19

MicroScope--an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res (2012) 5.12

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia. Nature (2006) 5.06

The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature (2011) 4.94

Evidence in the Legionella pneumophila genome for exploitation of host cell functions and high genome plasticity. Nat Genet (2004) 4.93

Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease. Mol Microbiol (2002) 4.82

A putative flip-flop switch for control of REM sleep. Nature (2006) 4.67

Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol (2003) 4.64

A role for RNAi in the selective correction of DNA methylation defects. Science (2009) 4.30

Unique features revealed by the genome sequence of Acinetobacter sp. ADP1, a versatile and naturally transformation competent bacterium. Nucleic Acids Res (2004) 4.19

Tools for the automatic identification and classification of RNA base pairs. Nucleic Acids Res (2003) 4.12

Nitrite-driven anaerobic methane oxidation by oxygenic bacteria. Nature (2010) 4.06

Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature (2006) 4.06

Comparative analysis of Acinetobacters: three genomes for three lifestyles. PLoS One (2008) 3.94

Aryl-aryl bond formation one century after the discovery of the Ullmann reaction. Chem Rev (2002) 3.65

The RNA Ontology Consortium: an open invitation to the RNA community. RNA (2006) 3.60

The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature (2010) 3.60

Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome. Proc Natl Acad Sci U S A (2003) 3.55

Non mycobacterial virulence genes in the genome of the emerging pathogen Mycobacterium abscessus. PLoS One (2009) 3.53

The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature (2012) 3.53

Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea. PLoS Genet (2011) 3.52

The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science (2006) 3.50

The genome of Theobroma cacao. Nat Genet (2010) 3.47

Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res (2007) 3.45

Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science (2007) 3.42

Comparative genomics and molecular dynamics of DNA repeats in eukaryotes. Microbiol Mol Biol Rev (2008) 3.35

Total synthesis of a functional designer eukaryotic chromosome. Science (2014) 3.31

Polydnaviruses of braconid wasps derive from an ancestral nudivirus. Science (2009) 3.29

Vector integration is nonrandom and clustered and influences the fate of lymphopoiesis in SCID-X1 gene therapy. J Clin Invest (2007) 3.28

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci U S A (2012) 3.26

Topology of three-way junctions in folded RNAs. RNA (2006) 3.14

Mapping the epigenetic basis of complex traits. Science (2014) 3.13

Genome sequences of Escherichia coli B strains REL606 and BL21(DE3). J Mol Biol (2009) 3.10

A human-curated annotation of the Candida albicans genome. PLoS Genet (2005) 3.04