Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

The yak genome and adaptation to life at high altitude

(2012) Qiang Qiu et al.   NATURE GENETICS

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

(2012) D. Floudas et al.   SCIENCE

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

Determining the evolutionary history of gene families

(2011) Ryan M. Ames et al.   BIOINFORMATICS

BadiRate: estimating family turnover rates by likelihood-based methods

(2011) P. Librado et al.   BIOINFORMATICS

A Bayesian model for gene family evolution

(2011) Liang Liu et al.   BMC BIOINFORMATICS

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster

(2011) D. R. Schrider et al.   GENOME RESEARCH

The evolution of gene expression levels in mammalian organs

(2011) David Brawand et al.   NATURE

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

Error and Error Mitigation in Low-Coverage Genome Assemblies

(2011) Melissa J. Hubisz et al.   PLoS One

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

Rapid Expansion and Functional Divergence of Subtelomeric Gene Families in Yeasts

(2010) Chris A. Brown et al.   CURRENT BIOLOGY

A Bayesian Approach for Fast and Accurate Gene Tree Reconstruction

(2010) M. D. Rasmussen et al.   MOLECULAR BIOLOGY AND EVOLUTION

The life and death of gene families

(2009) Jeffery P. Demuth et al.   BIOESSAYS

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

(2009) T. J. Sharpton et al.   GENOME RESEARCH

A burst of segmental duplications in the genome of the African great ape ancestor

(2009) Tomas Marques-Bonet et al.   NATURE

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

Estimating the Single Nucleotide Polymorphism Genotype Misclassification From Routine Double Measurements in a Large Epidemiologic Sample

(2008) I. M. Heid et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

(2008) F. Martin et al.   NATURE

Mapping and sequencing of structural variation from eight human genomes

(2008) Jeffrey M. Kidd et al.   NATURE

Natural Selection Shapes Genome-Wide Patterns of Copy-Number Polymorphism in Drosophila melanogaster

(2008) J. J. Emerson et al.   SCIENCE