Published in BMC Genomics on September 02, 2016
Basic local alignment search tool. J Mol Biol (1990) 659.07
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
Inference of population structure using multilocus genotype data. Genetics (2000) 147.76
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
Global variation in copy number in the human genome. Nature (2006) 57.50
Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol (2005) 55.64
Structural variation in the human genome. Nat Rev Genet (2006) 21.40
VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Res (2012) 15.90
Diversity of human copy number variation and multicopy genes. Science (2010) 8.97
REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS One (2011) 8.65
Diet and the evolution of human amylase gene copy number variation. Nat Genet (2007) 8.64
InterProScan 5: genome-scale protein function classification. Bioinformatics (2014) 8.52
Copy number variation in human health, disease, and evolution. Annu Rev Genomics Hum Genet (2009) 7.64
Genomic disorders: molecular mechanisms for rearrangements and conveyed phenotypes. PLoS Genet (2005) 7.60
Hidden killers: human fungal infections. Sci Transl Med (2012) 7.10
GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis. Nucleic Acids Res (2008) 6.91
The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res (2015) 5.97
Copy number variations and clinical cytogenetic diagnosis of constitutional disorders. Nat Genet (2007) 4.10
Aneuploidy and isochromosome formation in drug-resistant Candida albicans. Science (2006) 4.09
The impact of L1 retrotransposons on the human genome. Nat Genet (1998) 3.56
Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet (2014) 3.52
adegenet 1.3-1: new tools for the analysis of genome-wide SNP data. Bioinformatics (2011) 3.18
Cyclic AMP-dependent protein kinase controls virulence of the fungal pathogen Cryptococcus neoformans. Mol Cell Biol (2001) 3.11
The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line. Nat Biotechnol (2011) 2.87
Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data. Bioinformatics (2011) 2.86
Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization. Bioinformatics (2010) 2.79
Systematic genetic analysis of virulence in the human fungal pathogen Cryptococcus neoformans. Cell (2008) 2.71
Emergence and pathogenicity of highly virulent Cryptococcus gattii genotypes in the northwest United States. PLoS Pathog (2010) 2.67
Copy number variants, diseases and gene expression. Hum Mol Genet (2009) 2.66
Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science (2010) 2.62
A Streptococcus pneumoniae pathogenicity island encoding an ABC transporter involved in iron uptake and virulence. Mol Microbiol (2001) 2.55
A high-definition view of functional genetic variation from natural yeast genomes. Mol Biol Evol (2014) 2.10
Expanding fungal pathogenesis: Cryptococcus breaks out of the opportunistic box. Nat Rev Microbiol (2011) 2.05
Adaptive copy number evolution in malaria parasites. PLoS Genet (2008) 2.04
Copy number variation of multiple genes at Rhg1 mediates nematode resistance in soybean. Science (2012) 2.01
The capsule of the fungal pathogen Cryptococcus neoformans. Adv Appl Microbiol (2009) 1.97
The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome. Genetics (2003) 1.94
A unique fungal two-component system regulates stress responses, drug sensitivity, sexual development, and virulence of Cryptococcus neoformans. Mol Biol Cell (2006) 1.86
Gene copy-number alterations: a cost-benefit analysis. Cell (2013) 1.79
Large multiallelic copy number variations in humans. Nat Genet (2015) 1.79
Phospholipase activity in Cryptococcus neoformans: a new virulence factor? J Infect Dis (1997) 1.72
A copy number variation map of the human genome. Nat Rev Genet (2015) 1.68
Cryptococcus neoformans virulence gene discovery through insertional mutagenesis. Eukaryot Cell (2004) 1.68
Aluminum tolerance in maize is associated with higher MATE1 gene copy number. Proc Natl Acad Sci U S A (2013) 1.63
Copy number variation of individual cattle genomes using next-generation sequencing. Genome Res (2012) 1.62
Adenylyl cyclase-associated protein Aca1 regulates virulence and differentiation of Cryptococcus neoformans via the cyclic AMP-protein kinase A cascade. Eukaryot Cell (2004) 1.59
Properties and rates of germline mutations in humans. Trends Genet (2013) 1.58
Copy number variation and transcriptional polymorphisms of Phytophthora sojae RXLR effector genes Avr1a and Avr3a. PLoS One (2009) 1.51
Ras1 and Ras2 contribute shared and unique roles in physiology and virulence of Cryptococcus neoformans. Microbiology (2002) 1.51
Global diversity, population stratification, and selection of human copy-number variation. Science (2015) 1.48
HapX positively and negatively regulates the transcriptional response to iron deprivation in Cryptococcus neoformans. PLoS Pathog (2010) 1.47
Cryptococcus gattii in North American Pacific Northwest: whole-population genome analysis provides insights into species evolution and dispersal. MBio (2014) 1.45
Copy number variation in the bovine genome. BMC Genomics (2010) 1.45
Cryptococcus neoformans Kin1 protein kinase homologue, identified through a Caenorhabditis elegans screen, promotes virulence in mammals. Mol Microbiol (2004) 1.39
Adaptive evolution by mutations in the FLO11 gene. Proc Natl Acad Sci U S A (2006) 1.38
Evaluating ortholog prediction algorithms in a yeast model clade. PLoS One (2011) 1.37
Whole genome sequence analysis of Cryptococcus gattii from the Pacific Northwest reveals unexpected diversity. PLoS One (2011) 1.33
Role of a CUF1/CTR4 copper regulatory axis in the virulence of Cryptococcus neoformans. J Clin Invest (2007) 1.32
Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication. BMC Genomics (2013) 1.28
Copy number variation at the GL7 locus contributes to grain size diversity in rice. Nat Genet (2015) 1.27
Identification and characterization of a Cryptococcus neoformans ATP binding cassette (ABC) transporter-encoding gene, CnAFR1, involved in the resistance to fluconazole. Mol Microbiol (2003) 1.25
The Cryptococcus neoformans catalase gene family and its role in antioxidant defense. Eukaryot Cell (2006) 1.24
Characterization of Cu,Zn superoxide dismutase (SOD1) gene knock-out mutant of Cryptococcus neoformans var. gattii: role in biology and virulence. Mol Microbiol (2003) 1.23
The trehalose synthesis pathway is an integral part of the virulence composite for Cryptococcus gattii. Infect Immun (2009) 1.21
Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest. PLoS One (2013) 1.15
Phospholipase B activity enhances adhesion of Cryptococcus neoformans to a human lung epithelial cell line. Microbes Infect (2006) 1.11
The Cryptococcus neoformans transcriptome at the site of human meningitis. MBio (2014) 1.11
Identification of ENA1 as a virulence gene of the human pathogenic fungus Cryptococcus neoformans through signature-tagged insertional mutagenesis. Eukaryot Cell (2009) 1.11
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
Zap1 regulates zinc homeostasis and modulates virulence in Cryptococcus gattii. PLoS One (2012) 1.07
Novel origins of copy number variation in the dog genome. Genome Biol (2012) 1.06
Variation in chromosome copy number influences the virulence of Cryptococcus neoformans and occurs in isolates from AIDS patients. BMC Genomics (2011) 1.06
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
The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae. Curr Biol (2012) 1.02
Transcription factor STE12alpha has distinct roles in morphogenesis, virulence, and ecological fitness of the primary pathogenic yeast Cryptococcus gattii. Eukaryot Cell (2006) 1.01
Role of an expanded inositol transporter repertoire in Cryptococcus neoformans sexual reproduction and virulence. MBio (2010) 1.01
Highly recombinant VGII Cryptococcus gattii population develops clonal outbreak clusters through both sexual macroevolution and asexual microevolution. MBio (2014) 1.00
Role of AFR1, an ABC transporter-encoding gene, in the in vivo response to fluconazole and virulence of Cryptococcus neoformans. Infect Immun (2006) 1.00
Chromosomal copy number variation, selection and uneven rates of recombination reveal cryptic genome diversity linked to pathogenicity. PLoS Genet (2013) 0.99
Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii. MBio (2015) 0.99
Gene copy-number variation in haploid and diploid strains of the yeast Saccharomyces cerevisiae. Genetics (2013) 0.98
Cryptococcus gattii, no longer an accidental pathogen? Curr Fungal Infect Rep (2012) 0.97
A domain-centric solution to functional genomics via dcGO Predictor. BMC Bioinformatics (2013) 0.95
Current analysis platforms and methods for detecting copy number variation. Physiol Genomics (2012) 0.94
The exomer cargo adaptor structure reveals a novel GTPase-binding domain. EMBO J (2012) 0.92
The cAMP/Protein Kinase A Pathway and Virulence in Cryptococcus neoformans. Mycobiology (2011) 0.91
Genomic evidence for adaptation by gene duplication. Genome Res (2014) 0.90
Microreview: capsule-associated genes of Cryptococcus neoformans. Mycopathologia (2007) 0.90
Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions. Genome Res (2015) 0.87
DNA vaccination with a gene encoding Toxoplasma gondii Deoxyribose Phosphate Aldolase (TgDPA) induces partial protective immunity against lethal challenge in mice. Parasit Vectors (2014) 0.87
The human genome puzzle - the role of copy number variation in somatic mosaicism. Curr Genomics (2010) 0.87
Copy number variation in the horse genome. PLoS Genet (2014) 0.86
A murine model of Cryptococcus gattii meningoencephalitis. J Antimicrob Chemother (2012) 0.85
Effects of zinc transporters on Cryptococcus gattii virulence. Sci Rep (2015) 0.84
Cryptococcus gattii urease as a virulence factor and the relevance of enzymatic activity in cryptococcosis pathogenesis. FEBS J (2015) 0.84
Azole resistance in Cryptococcus gattii from the Pacific Northwest: Investigation of the role of ERG11. Antimicrob Agents Chemother (2013) 0.83
RNA interference in Cryptococcus neoformans. Methods Mol Biol (2012) 0.83
Population genetic nature of copy number variation. Methods Mol Biol (2012) 0.83
What makes Cryptococcus gattii a pathogen? FEMS Yeast Res (2015) 0.83
The coalescent with selection on copy number variants. Genetics (2011) 0.82