Heterogeneous rates of genome rearrangement contributed to the disparity of species richness in Ascomycota

GRIDSS: sensitive and specific genomic rearrangement detection using positional de Bruijn graph assembly

(2017) Daniel L. Cameron et al.   GENOME RESEARCH

Domestication and Divergence of Saccharomyces cerevisiae Beer Yeasts

(2016) Brigida Gallone et al.   CELL

Genomics and the making of yeast biodiversity

(2015) Chris Todd Hittinger et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

Genome rearrangements and pervasive meiotic drive cause hybrid infertility in fission yeast

(2014) Sarah E Zanders et al.   eLife

Breakpoint profiling of 64 cancer genomes reveals numerous complex rearrangements spawned by homology-independent mechanisms

(2013) A. Malhotra et al.   GENOME RESEARCH

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

(2013) R. de Jonge et al.   GENOME RESEARCH

Dating the Diversification of the Major Lineages of Ascomycota (Fungi)

(2013) María Prieto et al.   PLoS One

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis , Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

(2013) Viola A. Manning et al.   G3-Genes Genomes Genetics

YAHA: fast and flexible long-read alignment with optimal breakpoint detection

(2012) G. G. Faust et al.   BIOINFORMATICS

Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly

(2012) H. Li   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Genome evolution in filamentous plant pathogens: why bigger can be better

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

Clade Age and Species Richness Are Decoupled Across the Eukaryotic Tree of Life

(2012) Daniel L. Rabosky et al.   PLOS BIOLOGY

Transposable elements in yeasts

(2011) Claudine Bleykasten-Grosshans et al.   COMPTES RENDUS BIOLOGIES

Yeasty clocks: Dating genomic changes in yeasts

(2011) Thomas Rolland et al.   COMPTES RENDUS BIOLOGIES

LTR Retrotransposons in Fungi

(2011) Anna Muszewska et al.   PLoS One

Comparative Functional Genomics of the Fission Yeasts

(2011) N. Rhind et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Genome Rearrangements of Completely Sequenced Strains of Yersinia pestis

(2010) Y. Liang et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Yeast evolutionary genomics

(2010) Bernard Dujon   NATURE REVIEWS GENETICS

Chromosomal speciation revisited: rearranging theory with pieces of evidence

(2010) Rui Faria et al.   TRENDS IN ECOLOGY & EVOLUTION

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Ecological limits and diversification rate: alternative paradigms to explain the variation in species richness among clades and regions

(2009) Daniel L. Rabosky   ECOLOGY LETTERS

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

(2009) F. Hormozdiari et al.   GENOME RESEARCH

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

Computational methods for discovering structural variation with next-generation sequencing

(2009) Paul Medvedev et al.   NATURE METHODS

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

(2009) Conrad L. Schoch et al.   SYSTEMATIC BIOLOGY

Additions, Losses, and Rearrangements on the Evolutionary Route from a Reconstructed Ancestor to the Modern Saccharomyces cerevisiae Genome

(2009) Jonathan L. Gordon et al.   PLoS Genetics

PEMer: a computational framework with simulation-based error models for inferring genomic structural variants from massive paired-end sequencing data

(2009) Jan O Korbel et al.   GENOME BIOLOGY

Population genomics of the wild yeast Saccharomyces paradoxus: Quantifying the life cycle

(2008) I. J. Tsai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A genome-wide view of the spectrum of spontaneous mutations in yeast

(2008) M. Lynch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA