Published in Science on January 13, 2005
A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis. BMC Evol Biol (2006) 4.03
Iron regulation of the major virulence factors in the AIDS-associated pathogen Cryptococcus neoformans. PLoS Biol (2006) 3.43
A human-curated annotation of the Candida albicans genome. PLoS Genet (2005) 3.04
Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans. Cell (2008) 2.71
Diverse lifestyles and strategies of plant pathogenesis encoded in the genomes of eighteen Dothideomycetes fungi. PLoS Pathog (2012) 2.66
Genome sequence of the model mushroom Schizophyllum commune. Nat Biotechnol (2010) 2.44
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
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea (Coprinus cinereus). Proc Natl Acad Sci U S A (2010) 2.30
Yeast evolutionary genomics. Nat Rev Genet (2010) 2.27
Multilocus sequence typing reveals three genetic subpopulations of Cryptococcus neoformans var. grubii (serotype A), including a unique population in Botswana. Genetics (2005) 2.16
Specialization of the HOG pathway and its impact on differentiation and virulence of Cryptococcus neoformans. Mol Biol Cell (2005) 2.12
Highly efficient concerted evolution in the ribosomal DNA repeats: total rDNA repeat variation revealed by whole-genome shotgun sequence data. Genome Res (2007) 2.04
Comparative genomics of protoploid Saccharomycetaceae. Genome Res (2009) 1.96
Stalled spliceosomes are a signal for RNAi-mediated genome defense. Cell (2013) 1.94
Cryptococcus neoformans gene expression during murine macrophage infection. Eukaryot Cell (2005) 1.89
Unisexual and heterosexual meiotic reproduction generate aneuploidy and phenotypic diversity de novo in the yeast Cryptococcus neoformans. PLoS Biol (2013) 1.88
Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing. Nucleic Acids Res (2010) 1.87
A unique fungal two-component system regulates stress responses, drug sensitivity, sexual development, and virulence of Cryptococcus neoformans. Mol Biol Cell (2006) 1.86
Comparative gene genealogies indicate that two clonal lineages of Cryptococcus gattii in British Columbia resemble strains from other geographical areas. Eukaryot Cell (2005) 1.80
Chitosan, the deacetylated form of chitin, is necessary for cell wall integrity in Cryptococcus neoformans. Eukaryot Cell (2007) 1.76
A chitin synthase and its regulator protein are critical for chitosan production and growth of the fungal pathogen Cryptococcus neoformans. Eukaryot Cell (2005) 1.76
Genome variation in Cryptococcus gattii, an emerging pathogen of immunocompetent hosts. MBio (2011) 1.76
Genome-wide fitness test and mechanism-of-action studies of inhibitory compounds in Candida albicans. PLoS Pathog (2007) 1.74
Iron source preference and regulation of iron uptake in Cryptococcus neoformans. PLoS Pathog (2008) 1.65
Comparative genomic analysis of fungal genomes reveals intron-rich ancestors. Genome Biol (2007) 1.63
Analysis of the genome and transcriptome of Cryptococcus neoformans var. grubii reveals complex RNA expression and microevolution leading to virulence attenuation. PLoS Genet (2014) 1.62
Genetic diversity of the Cryptococcus species complex suggests that Cryptococcus gattii deserves to have varieties. PLoS One (2009) 1.56
Fungal secretome database: integrated platform for annotation of fungal secretomes. BMC Genomics (2010) 1.55
Molecular epidemiology of clinical Cryptococcus neoformans strains from India. J Clin Microbiol (2005) 1.53
alpha AD alpha hybrids of Cryptococcus neoformans: evidence of same-sex mating in nature and hybrid fitness. PLoS Genet (2007) 1.52
G protein-coupled receptor Gpr4 senses amino acids and activates the cAMP-PKA pathway in Cryptococcus neoformans. Mol Biol Cell (2005) 1.50
Fungal cytochrome P450 database. BMC Genomics (2008) 1.48
Genome characterization of the oleaginous fungus Mortierella alpina. PLoS One (2011) 1.43
How sweet it is! Cell wall biogenesis and polysaccharide capsule formation in Cryptococcus neoformans. Annu Rev Microbiol (2009) 1.43
Cryptococcus neoformans senses CO2 through the carbonic anhydrase Can2 and the adenylyl cyclase Cac1. Eukaryot Cell (2006) 1.41
Phylogenetic diversity of stress signalling pathways in fungi. BMC Evol Biol (2009) 1.40
Virulence attributes and hyphal growth of C. neoformans are quantitative traits and the MATalpha allele enhances filamentation. PLoS Genet (2006) 1.40
CFGP: a web-based, comparative fungal genomics platform. Nucleic Acids Res (2007) 1.39
Loss of cell wall alpha(1-3) glucan affects Cryptococcus neoformans from ultrastructure to virulence. Mol Microbiol (2007) 1.38
Basidiomycete mating type genes and pheromone signaling. Eukaryot Cell (2010) 1.37
Cross-kingdom patterns of alternative splicing and splice recognition. Genome Biol (2008) 1.36
Diploids in the Cryptococcus neoformans serotype A population homozygous for the alpha mating type originate via unisexual mating. PLoS Pathog (2009) 1.35
Sex-induced silencing defends the genome of Cryptococcus neoformans via RNAi. Genes Dev (2010) 1.35
Heteroresistance to fluconazole in Cryptococcus neoformans is intrinsic and associated with virulence. Antimicrob Agents Chemother (2009) 1.31
Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing. BMC Evol Biol (2007) 1.30
Transcription factors Mat2 and Znf2 operate cellular circuits orchestrating opposite- and same-sex mating in Cryptococcus neoformans. PLoS Genet (2010) 1.28
Very little intron loss/gain in Plasmodium: intron loss/gain mutation rates and intron number. Genome Res (2006) 1.26
Conrad: gene prediction using conditional random fields. Genome Res (2007) 1.26
Recombination hotspots flank the Cryptococcus mating-type locus: implications for the evolution of a fungal sex chromosome. PLoS Genet (2006) 1.24
Cryptococcus neoformans, a fungus under stress. Curr Opin Microbiol (2007) 1.24
G protein signaling governing cell fate decisions involves opposing Galpha subunits in Cryptococcus neoformans. Mol Biol Cell (2007) 1.24
Diversity of sesquiterpene synthases in the basidiomycete Coprinus cinereus. Mol Microbiol (2009) 1.22
Mechanisms of intron gain and loss in Cryptococcus. Genome Biol (2008) 1.21
Antifungal drug resistance of oral fungi. Odontology (2010) 1.21
Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using Deep RNA sequencing. PLoS One (2012) 1.19
Cryptococcus neoformans and Cryptococcus gattii, the etiologic agents of cryptococcosis. Cold Spring Harb Perspect Med (2014) 1.18
Eca1, a sarcoplasmic/endoplasmic reticulum Ca2+-ATPase, is involved in stress tolerance and virulence in Cryptococcus neoformans. Infect Immun (2007) 1.17
Particle-size distributions and seasonal diversity of allergenic and pathogenic fungi in outdoor air. ISME J (2012) 1.17
Nonlytic exocytosis of Cryptococcus neoformans from macrophages occurs in vivo and is influenced by phagosomal pH. MBio (2011) 1.15
Comparative genomics and genome evolution in yeasts. Philos Trans R Soc Lond B Biol Sci (2006) 1.15
Generation, annotation and analysis of ESTs from Trichoderma harzianum CECT 2413. BMC Genomics (2006) 1.15
Cryptococcus neoformans gene involved in mammalian pathogenesis identified by a Caenorhabditis elegans progeny-based approach. Infect Immun (2005) 1.13
Comparative genomics and the evolution of pathogenicity in human pathogenic fungi. Eukaryot Cell (2010) 1.13
Kinomer v. 1.0: a database of systematically classified eukaryotic protein kinases. Nucleic Acids Res (2008) 1.12
CPS1, a homolog of the Streptococcus pneumoniae type 3 polysaccharide synthase gene, is important for the pathobiology of Cryptococcus neoformans. Infect Immun (2006) 1.12
Identification of ENA1 as a virulence gene of the human pathogenic fungus Cryptococcus neoformans through signature-tagged insertional mutagenesis. Eukaryot Cell (2009) 1.11
Evolutionary role of interspecies hybridization and genetic exchanges in yeasts. Microbiol Mol Biol Rev (2012) 1.11
A Rac homolog functions downstream of Ras1 to control hyphal differentiation and high-temperature growth in the pathogenic fungus Cryptococcus neoformans. Eukaryot Cell (2005) 1.11
The Fusarium verticillioides FUM gene cluster encodes a Zn(II)2Cys6 protein that affects FUM gene expression and fumonisin production. Eukaryot Cell (2007) 1.11
Many globally isolated AD hybrid strains of Cryptococcus neoformans originated in Africa. PLoS Pathog (2007) 1.10
Peroxisome function regulates growth on glucose in the basidiomycete fungus Cryptococcus neoformans. Eukaryot Cell (2006) 1.10
Interaction between genetic background and the mating-type locus in Cryptococcus neoformans virulence potential. Genetics (2005) 1.10
Characterizing the role of RNA silencing components in Cryptococcus neoformans. Fungal Genet Biol (2010) 1.09
Impact of mating type, serotype, and ploidy on the virulence of Cryptococcus neoformans. Infect Immun (2008) 1.09
Whole genome and global gene expression analyses of the model mushroom Flammulina velutipes reveal a high capacity for lignocellulose degradation. PLoS One (2014) 1.08
Conserved elements of the RAM signaling pathway establish cell polarity in the basidiomycete Cryptococcus neoformans in a divergent fashion from other fungi. Mol Biol Cell (2006) 1.08
CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts. BMC Genomics (2015) 1.08
Canonical heterotrimeric G proteins regulating mating and virulence of Cryptococcus neoformans. Mol Biol Cell (2007) 1.08
The mating type locus (MAT) and sexual reproduction of Cryptococcus heveanensis: insights into the evolution of sex and sex-determining chromosomal regions in fungi. PLoS Genet (2010) 1.08
Exploration of whole-genome responses of the human AIDS-associated yeast pathogen Cryptococcus neoformans var grubii: nitric oxide stress and body temperature. Curr Genet (2007) 1.08
The copper regulon of the human fungal pathogen Cryptococcus neoformans H99. Mol Microbiol (2011) 1.08
Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans. Proc Natl Acad Sci U S A (2013) 1.07
Phylogeny and phenotypic characterization of pathogenic Cryptococcus species and closely related saprobic taxa in the Tremellales. Eukaryot Cell (2009) 1.07
Variation in chromosome copy number influences the virulence of Cryptococcus neoformans and occurs in isolates from AIDS patients. BMC Genomics (2011) 1.06
Gene discovery and transcript analyses in the corn smut pathogen Ustilago maydis: expressed sequence tag and genome sequence comparison. BMC Genomics (2007) 1.05
Drosophila and Galleria insect model hosts: new tools for the study of fungal virulence, pharmacology and immunology. Virulence (2011) 1.05
A tetrad analysis of the basidiomycete fungus Cryptococcus neoformans. Genetics (2010) 1.05
The pathogenic fungus Cryptococcus neoformans expresses two functional GDP-mannose transporters with distinct expression patterns and roles in capsule synthesis. Eukaryot Cell (2007) 1.05
Comparative hybridization reveals extensive genome variation in the AIDS-associated pathogen Cryptococcus neoformans. Genome Biol (2008) 1.05
Gene conversion occurs within the mating-type locus of Cryptococcus neoformans during sexual reproduction. PLoS Genet (2012) 1.04
Systems biology of fungal infection. Front Microbiol (2012) 1.04
Role of protein O-mannosyltransferase Pmt4 in the morphogenesis and virulence of Cryptococcus neoformans. Eukaryot Cell (2006) 1.04
The RGS protein Crg2 regulates both pheromone and cAMP signalling in Cryptococcus neoformans. Mol Microbiol (2008) 1.04
Regulatory diversity of TUP1 in Cryptococcus neoformans. Eukaryot Cell (2009) 1.03
Combination of amphotericin B with flucytosine is active in vitro against flucytosine-resistant isolates of Cryptococcus neoformans. Antimicrob Agents Chemother (2006) 1.03
Most environmental isolates of Cryptococcus neoformans var. grubii (serotype A) are not lethal for mice. Infect Immun (2009) 1.02
Survey and analysis of simple sequence repeats in the Laccaria bicolor genome, with development of microsatellite markers. Curr Genet (2010) 1.02
Multiple multi-copper oxidase gene families in basidiomycetes - what for? Curr Genomics (2011) 1.02
Chromosomal rearrangements between serotype A and D strains in Cryptococcus neoformans. PLoS One (2009) 1.02
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature (2004) 12.32
The diploid genome sequence of Candida albicans. Proc Natl Acad Sci U S A (2004) 6.34
Genome sequence of the lignocellulose degrading fungus Phanerochaete chrysosporium strain RP78. Nat Biotechnol (2004) 4.85
A molecular timescale of eukaryote evolution and the rise of complex multicellular life. BMC Evol Biol (2004) 4.17
Distribution of alpha and alpha mating types of Cryptococcus neoformans among natural and clinical isolates. Am J Epidemiol (1978) 3.55
Mating-type locus of Cryptococcus neoformans: a step in the evolution of sex chromosomes. Eukaryot Cell (2002) 3.12
A yeast under cover: the capsule of Cryptococcus neoformans. Eukaryot Cell (2003) 2.59
Melanin and virulence in Cryptococcus neoformans. Curr Opin Microbiol (2000) 2.24
beta-1,6-Glucan synthesis in Saccharomyces cerevisiae. Mol Microbiol (2000) 1.66
Structure of the chromosome VII centromere region in Neurospora crassa: degenerate transposons and simple repeats. Mol Cell Biol (1998) 1.42
Antisense repression in Cryptococcus neoformans as a laboratory tool and potential antifungal strategy. Microbiology (2002) 1.23
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
Versatile and open software for comparing large genomes. Genome Biol (2004) 49.45
Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics (2007) 47.63
ABySS: a parallel assembler for short read sequence data. Genome Res (2009) 43.20
Circos: an information aesthetic for comparative genomics. Genome Res (2009) 40.02
Genome sequence of the human malaria parasite Plasmodium falciparum. Nature (2002) 37.89
Functional profiling of the Saccharomyces cerevisiae genome. Nature (2002) 36.10
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol (2013) 32.42
UCHIME improves sensitivity and speed of chimera detection. Bioinformatics (2011) 29.22
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2007) 22.53
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2008) 21.36
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med (2013) 19.87
Assembling millions of short DNA sequences using SSAKE. Bioinformatics (2006) 18.71
Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature (2009) 18.08
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Fast algorithms for large-scale genome alignment and comparison. Nucleic Acids Res (2002) 17.31
Genomic responses in mouse models poorly mimic human inflammatory diseases. Proc Natl Acad Sci U S A (2013) 16.74
The Genome sequence of the SARS-associated coronavirus. Science (2003) 16.68
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". Proc Natl Acad Sci U S A (2005) 14.59
Slider--maximum use of probability information for alignment of short sequence reads and SNP detection. Bioinformatics (2008) 14.04
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics (2011) 13.71
The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol (2003) 13.32
ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med (2010) 13.07
A network-based analysis of systemic inflammation in humans. Nature (2005) 12.60
Quake: quality-aware detection and correction of sequencing errors. Genome Biol (2010) 12.52
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2009) 12.51
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet (2007) 12.21
Large-scale sequencing of human influenza reveals the dynamic nature of viral genome evolution. Nature (2005) 11.99
The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature (2012) 11.91
The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85
A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A (2006) 11.81
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
The genome of the African trypanosome Trypanosoma brucei. Science (2005) 11.48
Gene expression during the life cycle of Drosophila melanogaster. Science (2002) 11.36
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies. Nucleic Acids Res (2003) 11.03
Somatic mutations altering EZH2 (Tyr641) in follicular and diffuse large B-cell lymphomas of germinal-center origin. Nat Genet (2010) 10.97
Database resources of the National Center for Biotechnology Information. Nucleic Acids Res (2010) 10.97
The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature (2003) 10.38
Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells. Genome Res (2008) 10.18
Searching for SNPs with cloud computing. Genome Biol (2009) 10.12
Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis. Science (2002) 9.83
Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature (2010) 9.81
Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma. Nature (2011) 9.71
De novo assembly and analysis of RNA-seq data. Nat Methods (2010) 9.69
A comparison of whole-genome shotgun-derived mouse chromosome 16 and the human genome. Science (2002) 9.59
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 status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18