Copy number variation contributes to cryptic genetic variation in outbreak lineages of Cryptococcus gattii from the North American Pacific Northwest

Population-genetic properties of differentiated copy number variations in cattle

(2016) Lingyang Xu et al.   Scientific Reports

Genomic population structure and prevalence of copy number variations in South African Nguni cattle

(2015) Magretha Diane Wang et al.   BMC GENOMICS

Genomic copy number variation in Mus musculus

(2015) M Elizabeth O Locke et al.   BMC GENOMICS

Cryptococcus gattiiurease as a virulence factor and the relevance of enzymatic activity in cryptococcosis pathogenesis

(2015) Vanessa Feder et al.   FEBS Journal

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

(2015) Željka Pezer et al.   GENOME RESEARCH

High mutational rates of large-scale duplication and deletion inDaphnia pulex

(2015) Nathan Keith et al.   GENOME RESEARCH

Identification and properties of plasma membrane azole efflux pumps from the pathogenic fungiCryptococcus gattiiandCryptococcus neoformans

(2015) Luiz R. Basso et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Copy number variation at the GL7 locus contributes to grain size diversity in rice

(2015) Yuexing Wang et al.   NATURE GENETICS

Large multiallelic copy number variations in humans

(2015) Robert E Handsaker et al.   NATURE GENETICS

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Global diversity, population stratification, and selection of human copy-number variation

(2015) Peter H. Sudmant et al.   SCIENCE

Genome Evolution and Innovation across the Four Major Lineages of Cryptococcus gattii

(2015) Rhys A. Farrer et al.   mBio

Effects of zinc transporters on Cryptococcus gattii virulence

(2015) Rafael de Oliveira Schneider et al.   Scientific Reports

Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis

(2015) Jeanine M. Refsnider et al.   G3-Genes Genomes Genetics

Implementing a Class of Permutation Tests: ThecoinPackage

(2015) Torsten Hothorn et al.   Journal of Statistical Software

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Functional characterization of PMT2, encoding a protein-O-mannosyltransferase, in the human pathogen Cryptococcus neoformans

(2014) Kiminori Shimizu et al.   FUNGAL GENETICS AND BIOLOGY

Genomic evidence for adaptation by gene duplication

(2014) Wenfeng Qian et al.   GENOME RESEARCH

A High-Definition View of Functional Genetic Variation from Natural Yeast Genomes

(2014) Anders Bergström et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

DNA vaccination with a gene encoding Toxoplasma gondii Deoxyribose Phosphate Aldolase (TgDPA) induces partial protective immunity against lethal challenge in mice

(2014) Ibrahim A Hassan et al.   Parasites & Vectors

Highly Recombinant VGII Cryptococcus gattii Population Develops Clonal Outbreak Clusters through both Sexual Macroevolution and Asexual Microevolution

(2014) R. B. Billmyre et al.   mBio

Cryptococcus gattii in North American Pacific Northwest: Whole-Population Genome Analysis Provides Insights into Species Evolution and Dispersal

(2014) D. M. Engelthaler et al.   mBio

The Cryptococcus neoformans Transcriptome at the Site of Human Meningitis

(2014) Y. Chen et al.   mBio

Copy Number Variation in the Horse Genome

(2014) Sharmila Ghosh et al.   PLoS Genetics

Azole Resistance in Cryptococcus gattii from the Pacific Northwest: Investigation of the Role ofERG11

(2013) Charles E. Gast et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

(2013) Yogesh Paudel et al.   BMC GENOMICS

Gene Copy-Number Alterations: A Cost-Benefit Analysis

(2013) Yun-Chi Tang et al.   CELL

Gene Copy-Number Variation in Haploid and Diploid Strains of the Yeast Saccharomyces cerevisiae

(2013) H. Zhang et al.   GENETICS

Structural Basis of the Novel S. pneumoniae Virulence Factor, GHIP, a Glycosyl Hydrolase 25 Participating in Host-Cell Invasion

(2013) Siqiang Niu et al.   PLoS One

Ancient Dispersal of the Human Fungal Pathogen Cryptococcus gattii from the Amazon Rainforest

(2013) Ferry Hagen et al.   PLoS One

Aluminum tolerance in maize is associated with higher MATE1 gene copy number

(2013) L. G. Maron et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Properties and rates of germline mutations in humans

(2013) Catarina D. Campbell et al.   TRENDS IN GENETICS

Calcineurin Governs Thermotolerance and Virulence of Cryptococcus gattii

(2013) Ying-Lien Chen et al.   G3-Genes Genomes Genetics

Chromosomal Copy Number Variation, Selection and Uneven Rates of Recombination Reveal Cryptic Genome Diversity Linked to Pathogenicity

(2013) Rhys A. Farrer et al.   PLoS Genetics

The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae

(2012) John G. Gibbons et al.   CURRENT BIOLOGY

The exomer cargo adaptor structure reveals a novel GTPase-binding domain

(2012) Jon E Paczkowski et al.   EMBO JOURNAL

Copy number variation of individual cattle genomes using next-generation sequencing

(2012) D. M. Bickhart et al.   GENOME RESEARCH

VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing

(2012) D. C. Koboldt et al.   GENOME RESEARCH

A murine model of Cryptococcus gattii meningoencephalitis

(2012) G. R. Thompson et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Current analysis platforms and methods for detecting copy number variation

(2012) Wenli Li et al.   PHYSIOLOGICAL GENOMICS

Zap1 Regulates Zinc Homeostasis and Modulates Virulence in Cryptococcus gattii

(2012) Rafael de Oliveira Schneider et al.   PLoS One

Copy Number Variation of Multiple Genes at Rhg1 Mediates Nematode Resistance in Soybean

(2012) D. E. Cook et al.   SCIENCE

Hidden Killers: Human Fungal Infections

(2012) G. D. Brown et al.   Science Translational Medicine

Novel origins of copy number variation in the dog genome

(2012) Jonas Berglund et al.   GENOME BIOLOGY

The cAMP/Protein Kinase A Pathway and Virulence in Cryptococcus neoformans

(2012) James W. Kronstad et al.   MYCOBIOLOGY

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Variation in chromosome copy number influences the virulence of Cryptococcus neoformans and occurs in isolates from AIDS patients

(2011) Guanggan Hu et al.   BMC GENOMICS

The Coalescent with Selection on Copy Number Variants

(2011) K. M. Teshima et al.   GENETICS

The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Expanding fungal pathogenesis: Cryptococcus breaks out of the opportunistic box

(2011) James W. Kronstad et al.   NATURE REVIEWS MICROBIOLOGY

Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

(2011) Leonidas Salichos et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Whole Genome Sequence Analysis of Cryptococcus gattii from the Pacific Northwest Reveals Unexpected Diversity

(2011) John D. Gillece et al.   PLoS One

STRUCTURE HARVESTER: a website and program for visualizing STRUCTURE output and implementing the Evanno method

(2011) Dent A. Earl et al.   Conservation Genetics Resources

Control-free calling of copy number alterations in deep-sequencing data using GC-content normalization

(2010) Valentina Boeva et al.   BIOINFORMATICS

Copy number variation in the bovine genome

(2010) João Fadista et al.   BMC GENOMICS

The Human Genome Puzzle — the Role of Copy Number Variation in Somatic Mosaicism

(2010) Hasmik Mkrtchyan et al.   CURRENT GENOMICS

Diversity of Human Copy Number Variation and Multicopy Genes

(2010) Peter H. Sudmant et al.   SCIENCE

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

Emergence and Pathogenicity of Highly Virulent Cryptococcus gattii Genotypes in the Northwest United States

(2010) Edmond J. Byrnes et al.   PLoS Pathogens

HapX Positively and Negatively Regulates the Transcriptional Response to Iron Deprivation in Cryptococcus neoformans

(2010) Won Hee Jung et al.   PLoS Pathogens

Copy Number Variation in Human Health, Disease, and Evolution

(2009) Feng Zhang et al.   Annual Review of Genomics and Human Genetics

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Identification ofENA1as a Virulence Gene of the Human Pathogenic FungusCryptococcus neoformansthrough Signature-Tagged Insertional Mutagenesis

(2009) Alexander Idnurm et al.   EUKARYOTIC CELL

Copy number variants, diseases and gene expression

(2009) C. N. Henrichsen et al.   HUMAN MOLECULAR GENETICS

The Trehalose Synthesis Pathway Is an Integral Part of the Virulence Composite for Cryptococcus gattii

(2009) P. Ngamskulrungroj et al.   INFECTION AND IMMUNITY

Copy Number Variation and Transcriptional Polymorphisms of Phytophthora sojae RXLR Effector Genes Avr1a and Avr3a

(2009) Dinah Qutob et al.   PLoS One

Systematic Genetic Analysis of Virulence in the Human Fungal Pathogen Cryptococcus neoformans

(2008) Oliver W. Liu et al.   CELL

GOEAST: a web-based software toolkit for Gene Ontology enrichment analysis

(2008) Qi Zheng et al.   NUCLEIC ACIDS RESEARCH

Adaptive Copy Number Evolution in Malaria Parasites

(2008) Shalini Nair et al.   PLoS Genetics